2017
Leclercq, Mickael; Diallo, Abdoulaye Baniré; Blanchette, Mathieu
Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences Article de journal
Dans: Nucleic Acids Research, vol. 45, no 2, p. 556–566, 2017, ISSN: 0305-1048, 1362-4962.
@article{leclercq_prediction_2017,
title = {Prediction of human miRNA target genes using computationally reconstructed ancestral mammalian sequences},
author = {Mickael Leclercq and Abdoulaye Banir\'{e} Diallo and Mathieu Blanchette},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1085},
doi = {10.1093/nar/gkw1085},
issn = {0305-1048, 1362-4962},
year = {2017},
date = {2017-01-01},
urldate = {2024-04-30},
journal = {Nucleic Acids Research},
volume = {45},
number = {2},
pages = {556\textendash566},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2016
Dhifli, Wajdi; Diallo, Abdoulaye Baniré
ProtNN: fast and accurate protein 3D-structure classification in structural and topological space Article de journal
Dans: BioData Mining, vol. 9, no 1, p. 30, 2016, ISSN: 1756-0381.
@article{dhifli_protnn_2016,
title = {ProtNN: fast and accurate protein 3D-structure classification in structural and topological space},
author = {Wajdi Dhifli and Abdoulaye Banir\'{e} Diallo},
url = {http://biodatamining.biomedcentral.com/articles/10.1186/s13040-016-0108-2},
doi = {10.1186/s13040-016-0108-2},
issn = {1756-0381},
year = {2016},
date = {2016-12-01},
urldate = {2024-04-30},
journal = {BioData Mining},
volume = {9},
number = {1},
pages = {30},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Remita, Mohamed Amine; Lord, Etienne; Agharbaoui, Zahra; Leclercq, Mickael; Badawi, Mohamed A.; Sarhan, Fathey; Diallo, Abdoulaye Baniré
A novel comprehensive wheat miRNA database, including related bioinformatics software Article de journal
Dans: Current Plant Biology, vol. 7-8, p. 31–33, 2016, ISSN: 22146628.
@article{remita_novel_2016,
title = {A novel comprehensive wheat miRNA database, including related bioinformatics software},
author = {Mohamed Amine Remita and Etienne Lord and Zahra Agharbaoui and Mickael Leclercq and Mohamed A. Badawi and Fathey Sarhan and Abdoulaye Banir\'{e} Diallo},
url = {https://linkinghub.elsevier.com/retrieve/pii/S2214662816300299},
doi = {10.1016/j.cpb.2016.10.003},
issn = {22146628},
year = {2016},
date = {2016-11-01},
urldate = {2024-04-30},
journal = {Current Plant Biology},
volume = {7-8},
pages = {31\textendash33},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Remita, Mohamed Amine; Halioui, Ahmed; Diouara, Abou Abdallah Malick; Daigle, Bruno; Kiani, Golrokh; Diallo, Abdoulaye Baniré
CASTOR: A machine learning platform for reproducible viral genome classification Divers
2016.
@misc{remita_castor_2016,
title = {CASTOR: A machine learning platform for reproducible viral genome classification},
author = {Mohamed Amine Remita and Ahmed Halioui and Abou Abdallah Malick Diouara and Bruno Daigle and Golrokh Kiani and Abdoulaye Banir\'{e} Diallo},
url = {http://biorxiv.org/lookup/doi/10.1101/082768},
doi = {10.1101/082768},
year = {2016},
date = {2016-10-01},
urldate = {2024-04-30},
abstract = {Abstract
Motivation
Advances in cloning and sequencing technology yielded a massive number of genome of virus strains. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for a well-studied virus. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families.
Results
Here, we introduce a fast, accurate and generic virus classification platform, CASTOR, based on a machine learning approach. CASTOR is inspired by a well-known technique in molecular biology: Restriction Fragment Length Polymorphism (RFLP). It simulates the restriction digestion of genomic material by different enzymes into fragments in-silico. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of Human Papillomaviruses (HPV), Hepatitis B Viruses (HBV) and Human Immunodeficiency viruses (HIV). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV M group subtyping respectively. Furthermore, CASTOR shows a competitive performance compare to well-known HIV-specific classifier REGA and COMET on whole genome and
pol
fragments. With such prediction rates, genericity and robustness, as well as rapidity, such approach could constitute a reference in large-scale virus studies. Finally, we developed the CASTOR web platform for open access and reproducible viral machine learning classifiers.
Availability
http://castor.bioinfo.uqam.ca
Contact diallo.abdoulaye@uqam.ca},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Motivation
Advances in cloning and sequencing technology yielded a massive number of genome of virus strains. The classification and annotation of these genomes constitute important assets in the discovery of genomic variability, taxonomic characteristics and disease mechanisms. Existing classification methods are often designed for a well-studied virus. Thus, the viral comparative genomic studies could benefit from more generic, fast and accurate tools for classifying and typing newly sequenced strains of diverse virus families.
Results
Here, we introduce a fast, accurate and generic virus classification platform, CASTOR, based on a machine learning approach. CASTOR is inspired by a well-known technique in molecular biology: Restriction Fragment Length Polymorphism (RFLP). It simulates the restriction digestion of genomic material by different enzymes into fragments in-silico. It uses two metrics to construct feature vectors for machine learning algorithms in the classification step. We benchmark CASTOR for the classification of distinct datasets of Human Papillomaviruses (HPV), Hepatitis B Viruses (HBV) and Human Immunodeficiency viruses (HIV). Results reveal true positive rates of 99%, 99% and 98% for HPV Alpha species, HBV genotyping and HIV M group subtyping respectively. Furthermore, CASTOR shows a competitive performance compare to well-known HIV-specific classifier REGA and COMET on whole genome and
pol
fragments. With such prediction rates, genericity and robustness, as well as rapidity, such approach could constitute a reference in large-scale virus studies. Finally, we developed the CASTOR web platform for open access and reproducible viral machine learning classifiers.
Availability
http://castor.bioinfo.uqam.ca
Contact diallo.abdoulaye@uqam.ca
Halioui, Ahmed; Valtchev, Petko; Diallo, Abdoulaye Baniré
Towards an ontology-based recommender system for relevant bioinformatics workflows Divers
2016.
@misc{halioui_towards_2016,
title = {Towards an ontology-based recommender system for relevant bioinformatics workflows},
author = {Ahmed Halioui and Petko Valtchev and Abdoulaye Banir\'{e} Diallo},
url = {http://biorxiv.org/lookup/doi/10.1101/082776},
doi = {10.1101/082776},
year = {2016},
date = {2016-10-01},
urldate = {2024-04-30},
abstract = {Abstract
Background
With the large and diverse type of biological data, bioinformatic solutions are being more complex and computationally intensive. New specialized data skills need to be acquired by researchers in order to follow this development. Workflow Management Systems rise as an efficient way to automate tasks through abstract models in order to assist users during their problem solving tasks. However, current solutions could have several problems in reusing the developed models for given tasks. The large amount of heterogenous data and the lack of knowledge in using bioinformatics tools could mislead the users during their analyses. To tackle this issue, we propose an ontology-based workflow-mining framework generating semantic models of bioinformatic best practices in order to assist scientists. To this end, concrete workflows are extracted from scientific articles and then mined using a rich domain ontology.
Results
In this study, we explore the specific topics of phylogenetic analyses. We annotated more than 300 recent articles using different ontological concepts and relations. Relative supports (frequencies) of discovered workflow components in texts show interesting results of relevant resources currently used in the different phylogenetic analysis steps. Mining concrete workflows from texts lead us to discover abstract but relevant patterns of the best combinations of tools, parameters and input data for specific phylogenetic problems.
Conclusions
Extracted patterns would make workflows more intuitive and easy to be reused in similar situations. This could provide a stepping-stone into the identification of best practices and pave the road to a recommender system.},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Background
With the large and diverse type of biological data, bioinformatic solutions are being more complex and computationally intensive. New specialized data skills need to be acquired by researchers in order to follow this development. Workflow Management Systems rise as an efficient way to automate tasks through abstract models in order to assist users during their problem solving tasks. However, current solutions could have several problems in reusing the developed models for given tasks. The large amount of heterogenous data and the lack of knowledge in using bioinformatics tools could mislead the users during their analyses. To tackle this issue, we propose an ontology-based workflow-mining framework generating semantic models of bioinformatic best practices in order to assist scientists. To this end, concrete workflows are extracted from scientific articles and then mined using a rich domain ontology.
Results
In this study, we explore the specific topics of phylogenetic analyses. We annotated more than 300 recent articles using different ontological concepts and relations. Relative supports (frequencies) of discovered workflow components in texts show interesting results of relevant resources currently used in the different phylogenetic analysis steps. Mining concrete workflows from texts lead us to discover abstract but relevant patterns of the best combinations of tools, parameters and input data for specific phylogenetic problems.
Conclusions
Extracted patterns would make workflows more intuitive and easy to be reused in similar situations. This could provide a stepping-stone into the identification of best practices and pave the road to a recommender system.
Halioui, Ahmed; Valtchev, Petko; Diallo, Abdoulaye Baniré
Ontology-based workflow extraction from texts using word sense disambiguation Divers
2016.
@misc{halioui_ontology-based_2016,
title = {Ontology-based workflow extraction from texts using word sense disambiguation},
author = {Ahmed Halioui and Petko Valtchev and Abdoulaye Banir\'{e} Diallo},
url = {http://biorxiv.org/lookup/doi/10.1101/082784},
doi = {10.1101/082784},
year = {2016},
date = {2016-10-01},
urldate = {2024-04-30},
abstract = {Abstract
This paper introduces a method for automatic workflow extraction from texts using Process-Oriented Case-Based Reasoning (POCBR). While the current workflow management systems implement mostly different complicated graphical tasks based on advanced distributed solutions (
e.g.
cloud computing and grid computation), workflow knowledge acquisition from texts using case-based reasoning represents more expressive and semantic cases representations. We propose in this context, an ontology-based workflow extraction framework to acquire processual knowledge from texts. Our methodology extends classic NLP techniques to extract and disambiguate tasks in texts. Using a graph-based representation of workflows and a domain ontology, our extraction process uses a context-based approach to recognize workflow components : data and control flows. We applied our framework in a technical domain in bioinformatics : i.e. phylogenetic analyses. An evaluation based on workflow semantic similarities on a gold standard proves that our approach provides promising results in the process extraction domain. Both data and implementation of our framework are available in :
http://labo.bioinfo.uqam.ca/tgrowler
.},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
This paper introduces a method for automatic workflow extraction from texts using Process-Oriented Case-Based Reasoning (POCBR). While the current workflow management systems implement mostly different complicated graphical tasks based on advanced distributed solutions (
e.g.
cloud computing and grid computation), workflow knowledge acquisition from texts using case-based reasoning represents more expressive and semantic cases representations. We propose in this context, an ontology-based workflow extraction framework to acquire processual knowledge from texts. Our methodology extends classic NLP techniques to extract and disambiguate tasks in texts. Using a graph-based representation of workflows and a domain ontology, our extraction process uses a context-based approach to recognize workflow components : data and control flows. We applied our framework in a technical domain in bioinformatics : i.e. phylogenetic analyses. An evaluation based on workflow semantic similarities on a gold standard proves that our approach provides promising results in the process extraction domain. Both data and implementation of our framework are available in :
http://labo.bioinfo.uqam.ca/tgrowler
.
Dhifli, Wajdi; Diallo, Abdoulaye Baniré
Face Recognition in the Wild Article de journal
Dans: Procedia Computer Science, vol. 96, p. 1571–1580, 2016, ISSN: 18770509.
@article{dhifli_face_2016,
title = {Face Recognition in the Wild},
author = {Wajdi Dhifli and Abdoulaye Banir\'{e} Diallo},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1877050916320142},
doi = {10.1016/j.procs.2016.08.204},
issn = {18770509},
year = {2016},
date = {2016-01-01},
urldate = {2024-04-30},
journal = {Procedia Computer Science},
volume = {96},
pages = {1571\textendash1580},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2015
Lord, Etienne; Diallo, Abdoulaye Baniré; Makarenkov, Vladimir
Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms Article de journal
Dans: BMC Bioinformatics, vol. 16, no 1, p. 68, 2015, ISSN: 1471-2105.
@article{lord_classification_2015,
title = {Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms},
author = {Etienne Lord and Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0508-1},
doi = {10.1186/s12859-015-0508-1},
issn = {1471-2105},
year = {2015},
date = {2015-12-01},
urldate = {2024-04-30},
journal = {BMC Bioinformatics},
volume = {16},
number = {1},
pages = {68},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Agharbaoui, Zahra; Leclercq, Mickael; Remita, Mohamed Amine; Badawi, Mohamed A; Lord, Etienne; Houde, Mario; Danyluk, Jean; Diallo, Abdoulaye Baniré; Sarhan, Fathey
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress Article de journal
Dans: BMC Genomics, vol. 16, no 1, p. 339, 2015, ISSN: 1471-2164.
@article{agharbaoui_integrative_2015,
title = {An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress},
author = {Zahra Agharbaoui and Mickael Leclercq and Mohamed Amine Remita and Mohamed A Badawi and Etienne Lord and Mario Houde and Jean Danyluk and Abdoulaye Banir\'{e} Diallo and Fathey Sarhan},
url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1490-8},
doi = {10.1186/s12864-015-1490-8},
issn = {1471-2164},
year = {2015},
date = {2015-12-01},
urldate = {2024-04-30},
journal = {BMC Genomics},
volume = {16},
number = {1},
pages = {339},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Halioui, Ahmed; Valtchev, Petko; Diallo, Abdoulaye Banire
Acquisition of Generic Problem Solving Knowledge through Information Extraction and Pattern Mining Article d’actes
Dans: 2015 IEEE 27th International Conference on Tools with Artificial Intelligence (ICTAI), p. 583–590, IEEE, Vietri sul Mare, Italy, 2015, ISBN: 9781509001637.
@inproceedings{halioui_acquisition_2015,
title = {Acquisition of Generic Problem Solving Knowledge through Information Extraction and Pattern Mining},
author = {Ahmed Halioui and Petko Valtchev and Abdoulaye Banire Diallo},
url = {http://ieeexplore.ieee.org/document/7372186/},
doi = {10.1109/ICTAI.2015.90},
isbn = {9781509001637},
year = {2015},
date = {2015-11-01},
urldate = {2024-04-30},
booktitle = {2015 IEEE 27th International Conference on Tools with Artificial Intelligence (ICTAI)},
pages = {583\textendash590},
publisher = {IEEE},
address = {Vietri sul Mare, Italy},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Diallo, Abdoulaye Baniré; Agharbaoui, Zahra; Leclercq, Mickael; Remita, Mohamed Amine; Badawi, Mohamed; Houde, Mario; Sarhan, Fathey
Large scale identification of microRNAs associated with stress response and development in wheat Article de journal
Dans: 2015.
@article{abdoulaye_banire__diallo_large_2015,
title = {Large scale identification of microRNAs associated with stress response and development in wheat},
author = {Abdoulaye Banir\'{e} Diallo and Zahra Agharbaoui and Mickael Leclercq and Mohamed Amine Remita and Mohamed Badawi and Mario Houde and Fathey Sarhan},
url = {http://f1000research.com/posters/4-786},
doi = {10.7490/F1000RESEARCH.1110535.1},
year = {2015},
date = {2015-01-01},
urldate = {2024-04-30},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Daigle, Bruno; Makarenkov, Vladimir; Diallo, Abdoulaye Baniré
Effect of Hundreds Sequenced Genomes on the Classification of Human Papillomaviruses Section de livre
Dans: Lausen, Berthold; Krolak-Schwerdt, Sabine; Böhmer, Matthias (Ed.): Data Science, Learning by Latent Structures, and Knowledge Discovery, p. 309–318, Springer Berlin Heidelberg, Berlin, Heidelberg, 2015, ISBN: 9783662449820 9783662449837.
@incollection{lausen_effect_2015,
title = {Effect of Hundreds Sequenced Genomes on the Classification of Human Papillomaviruses},
author = {Bruno Daigle and Vladimir Makarenkov and Abdoulaye Banir\'{e} Diallo},
editor = {Berthold Lausen and Sabine Krolak-Schwerdt and Matthias B\"{o}hmer},
url = {https://link.springer.com/10.1007/978-3-662-44983-7_27},
doi = {10.1007/978-3-662-44983-7_27},
isbn = {9783662449820 9783662449837},
year = {2015},
date = {2015-01-01},
urldate = {2024-04-30},
booktitle = {Data Science, Learning by Latent Structures, and Knowledge Discovery},
pages = {309\textendash318},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Dhifli, Wajdi; Diallo, Abdoulaye Baniré
ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space Article de journal
Dans: 2015.
@article{dhifli_protnn_2015,
title = {ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space},
author = {Wajdi Dhifli and Abdoulaye Banir\'{e} Diallo},
url = {https://arxiv.org/abs/1511.00736},
doi = {10.48550/ARXIV.1511.00736},
year = {2015},
date = {2015-01-01},
urldate = {2024-04-30},
abstract = {Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Abdoulaye, Wajdi Dhifli
PGR: A Novel Graph Repository of Protein 3D-Structures Article de journal
Dans: Journal of Data Mining in Genomics & Proteomics, vol. 06, no 02, 2015, ISSN: 21530602.
@article{abdoulaye_pgr_2015,
title = {PGR: A Novel Graph Repository of Protein 3D-Structures},
author = {Wajdi Dhifli Abdoulaye},
url = {https://www.omicsonline.org/open-access/pgr-a-novel-graph-repository-of-protein-3dstructures-2153-0602-1000172.php?aid=56291},
doi = {10.4172/2153-0602.1000172},
issn = {21530602},
year = {2015},
date = {2015-01-01},
urldate = {2024-04-30},
journal = {Journal of Data Mining in Genomics \& Proteomics},
volume = {06},
number = {02},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Dhifli, Wajdi; Diallo, Abdoulaye Baniré
Toward an Efficient Multi-class Classification in an Open Universe Article de journal
Dans: 2015.
@article{dhifli_toward_2015,
title = {Toward an Efficient Multi-class Classification in an Open Universe},
author = {Wajdi Dhifli and Abdoulaye Banir\'{e} Diallo},
url = {https://arxiv.org/abs/1511.00725},
doi = {10.48550/ARXIV.1511.00725},
year = {2015},
date = {2015-01-01},
urldate = {2024-04-30},
abstract = {Classification is a fundamental task in machine learning and data mining. Existing classification methods are designed to classify unknown instances within a set of previously known training classes. Such a classification takes the form of a prediction within a closed-set of classes. However, a more realistic scenario that fits real-world applications is to consider the possibility of encountering instances that do not belong to any of the training classes, $i.e.$, an open-set classification. In such situation, existing closed-set classifiers will assign a training label to these instances resulting in a misclassification. In this paper, we introduce Galaxy-X, a novel multi-class classification approach for open-set recognition problems. For each class of the training set, Galaxy-X creates a minimum bounding hyper-sphere that encompasses the distribution of the class by enclosing all of its instances. In such manner, our method is able to distinguish instances resembling previously seen classes from those that are of unknown ones. To adequately evaluate open-set classification, we introduce a novel evaluation procedure. Experimental results on benchmark datasets show the efficiency of our approach in classifying novel instances from known as well as unknown classes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2014
Remita, Mohamed Amine; Halioui, Ahmed; Diallo, Abdoulaye Baniré
Supervised Classification of Viral Genomes based on Restriction Site Distribution Article de journal
Dans: 2014.
@article{remita_supervised_2014,
title = {Supervised Classification of Viral Genomes based on Restriction Site Distribution},
author = {Mohamed Amine Remita and Ahmed Halioui and Abdoulaye Banir\'{e} Diallo},
url = {http://rgdoi.net/10.13140/RG.2.1.3708.3763},
doi = {10.13140/RG.2.1.3708.3763},
year = {2014},
date = {2014-01-01},
urldate = {2024-04-30},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2013
Leclercq, Mickael; Diallo, Abdoulaye Banire; Blanchette, Mathieu
Computational prediction of the localization of microRNAs within their pre-miRNA Article de journal
Dans: Nucleic Acids Research, vol. 41, no 15, p. 7200–7211, 2013, ISSN: 1362-4962, 0305-1048.
@article{leclercq_computational_2013,
title = {Computational prediction of the localization of microRNAs within their pre-miRNA},
author = {Mickael Leclercq and Abdoulaye Banire Diallo and Mathieu Blanchette},
url = {https://academic.oup.com/nar/article/41/15/7200/2410969},
doi = {10.1093/nar/gkt466},
issn = {1362-4962, 0305-1048},
year = {2013},
date = {2013-08-01},
urldate = {2024-04-30},
journal = {Nucleic Acids Research},
volume = {41},
number = {15},
pages = {7200\textendash7211},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2012
Leiser, Willmar L.; Rattunde, H. Frederick W.; Piepho, Hans‐Peter; Weltzien, Eva; Diallo, Abdoulaye; Melchinger, Albrecht E.; Parzies, Heiko K.; Haussmann, Bettina I. G.
Selection Strategy for Sorghum Targeting Phosphorus‐limited Environments in West Africa: Analysis of Multi‐environment Experiments Article de journal
Dans: Crop Science, vol. 52, no 6, p. 2517–2527, 2012, ISSN: 0011-183X, 1435-0653.
@article{leiser_selection_2012,
title = {Selection Strategy for Sorghum Targeting Phosphorus‐limited Environments in West Africa: Analysis of Multi‐environment Experiments},
author = {Willmar L. Leiser and H. Frederick W. Rattunde and Hans‐Peter Piepho and Eva Weltzien and Abdoulaye Diallo and Albrecht E. Melchinger and Heiko K. Parzies and Bettina I. G. Haussmann},
url = {https://acsess.onlinelibrary.wiley.com/doi/10.2135/cropsci2012.02.0139},
doi = {10.2135/cropsci2012.02.0139},
issn = {0011-183X, 1435-0653},
year = {2012},
date = {2012-11-01},
urldate = {2024-04-30},
journal = {Crop Science},
volume = {52},
number = {6},
pages = {2517\textendash2527},
abstract = {ABSTRACT
Although sorghum [
Sorghum bicolor
(L.) Moench] in West Africa (WA) is generally cultivated with limited or no fertilization on soils of low phosphorus availability, no assessments of the genetic variation among WA sorghum varieties for adaptation to low soil P are known. We assessed grain yields of 70 diverse sorghum genotypes under −P (no P fertilization) and +P conditions at two locations in Mali over 5 yr. Genetic variation for grain yield under −P conditions and the feasibility and necessity of sorghum varietal testing for grain yield under −P conditions were evaluated. Delayed heading dates (0\textendash9.8 d) and reductions of grain yield (2\textendash59%) and plant height (13\textendash107 cm) were observed in −P relative to the +P trials. High estimates of genetic variance and broad‐sense heritabilities were found for grain yield across both −P (
h
2 = 0.93) and +P (
h
2 = 0.92) environments. The genetic correlation for grain yield performance between −P and +P conditions was high (
r
G = 0.89), suggesting that WA sorghum varieties generally possess good adaptation to low‐P conditions. However, genotype × phosphorus crossover interaction was observed between some of the highest yielding genotypes from the −P and +P selected sets, with the variety IS 15401 showing specific adaptation to −P. Direct selection for grain yield in −P conditions was predicted to be 12% more efficient than indirect selection in +P conditions. Thus, selection under −P conditions should be useful for sorghum improvement in WA.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Although sorghum [
Sorghum bicolor
(L.) Moench] in West Africa (WA) is generally cultivated with limited or no fertilization on soils of low phosphorus availability, no assessments of the genetic variation among WA sorghum varieties for adaptation to low soil P are known. We assessed grain yields of 70 diverse sorghum genotypes under −P (no P fertilization) and +P conditions at two locations in Mali over 5 yr. Genetic variation for grain yield under −P conditions and the feasibility and necessity of sorghum varietal testing for grain yield under −P conditions were evaluated. Delayed heading dates (0–9.8 d) and reductions of grain yield (2–59%) and plant height (13–107 cm) were observed in −P relative to the +P trials. High estimates of genetic variance and broad‐sense heritabilities were found for grain yield across both −P (
h
2 = 0.93) and +P (
h
2 = 0.92) environments. The genetic correlation for grain yield performance between −P and +P conditions was high (
r
G = 0.89), suggesting that WA sorghum varieties generally possess good adaptation to low‐P conditions. However, genotype × phosphorus crossover interaction was observed between some of the highest yielding genotypes from the −P and +P selected sets, with the variety IS 15401 showing specific adaptation to −P. Direct selection for grain yield in −P conditions was predicted to be 12% more efficient than indirect selection in +P conditions. Thus, selection under −P conditions should be useful for sorghum improvement in WA.
Boc, A.; Diallo, A. B.; Makarenkov, V.
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks Article de journal
Dans: Nucleic Acids Research, vol. 40, no W1, p. W573–W579, 2012, ISSN: 0305-1048, 1362-4962.
@article{boc_t-rex_2012,
title = {T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks},
author = {A. Boc and A. B. Diallo and V. Makarenkov},
url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gks485},
doi = {10.1093/nar/gks485},
issn = {0305-1048, 1362-4962},
year = {2012},
date = {2012-07-01},
urldate = {2024-04-30},
journal = {Nucleic Acids Research},
volume = {40},
number = {W1},
pages = {W573\textendashW579},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lord, Etienne; Leclercq, Mickael; Boc, Alix; Diallo, Abdoulaye Baniré; Makarenkov, Vladimir
Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations Article de journal
Dans: PLoS ONE, vol. 7, no 1, p. e29903, 2012, ISSN: 1932-6203.
@article{lord_armadillo_2012,
title = {Armadillo 1.1: An Original Workflow Platform for Designing and Conducting Phylogenetic Analysis and Simulations},
author = {Etienne Lord and Mickael Leclercq and Alix Boc and Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov},
editor = {Simon Joly},
url = {https://dx.plos.org/10.1371/journal.pone.0029903},
doi = {10.1371/journal.pone.0029903},
issn = {1932-6203},
year = {2012},
date = {2012-01-01},
urldate = {2024-04-30},
journal = {PLoS ONE},
volume = {7},
number = {1},
pages = {e29903},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2011
Badescu, Dunarel; Boc, Alix; Diallo, Abdoulaye Baniré; Makarenkov, Vladimir
Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index Article de journal
Dans: BMC Bioinformatics, vol. 12, no S9, p. S9, 2011, ISSN: 1471-2105.
@article{badescu_detecting_2011,
title = {Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index},
author = {Dunarel Badescu and Alix Boc and Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-S9-S9},
doi = {10.1186/1471-2105-12-S9-S9},
issn = {1471-2105},
year = {2011},
date = {2011-12-01},
urldate = {2024-04-30},
journal = {BMC Bioinformatics},
volume = {12},
number = {S9},
pages = {S9},
abstract = {Abstract
Background
The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of conserved regions and motifs. However, most of existing methods ignore the relationship between the functional genomic regions and the external evidence associated with the considered group of species (e.g., carcinogenicity of Human Papilloma Virus). In the past, we have proposed a method that takes into account the prior knowledge on an external evidence (e.g., carcinogenicity or invasivity of the considered organisms) and identifies genomic regions related to a specific disease.
Results and conclusion
We present a new algorithm for detecting genomic regions that may be associated with a disease. Two new variability functions and a bipartition optimization procedure are described. We validate and weigh our results using the Adjusted Rand Index (ARI), and thus assess to what extent the selected regions are related to carcinogenicity, invasivity, or any other species classification, given as input. The predictive power of different hit region detection functions was assessed on synthetic and real data. Our simulation results suggest that there is no a single function that provides the best results in all practical situations (e.g., monophyletic or polyphyletic evolution, and positive or negative selection), and that at least three different functions might be useful. The proposed hit region identification functions that do not benefit from the prior knowledge (i.e., carcinogenicity or invasivity of the involved organisms) can provide equivalent results than the existing functions that take advantage of such a prior knowledge. Using the new algorithm, we examined the
Neisseria meningitidis
FrpB gene product for invasivity and immunologic activity, and human papilloma virus (HPV) E6 oncoprotein for carcinogenicity, and confirmed some well-known molecular features, including surface exposed loops for
N. meningitidis
and PDZ domain for HPV.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background
The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of conserved regions and motifs. However, most of existing methods ignore the relationship between the functional genomic regions and the external evidence associated with the considered group of species (e.g., carcinogenicity of Human Papilloma Virus). In the past, we have proposed a method that takes into account the prior knowledge on an external evidence (e.g., carcinogenicity or invasivity of the considered organisms) and identifies genomic regions related to a specific disease.
Results and conclusion
We present a new algorithm for detecting genomic regions that may be associated with a disease. Two new variability functions and a bipartition optimization procedure are described. We validate and weigh our results using the Adjusted Rand Index (ARI), and thus assess to what extent the selected regions are related to carcinogenicity, invasivity, or any other species classification, given as input. The predictive power of different hit region detection functions was assessed on synthetic and real data. Our simulation results suggest that there is no a single function that provides the best results in all practical situations (e.g., monophyletic or polyphyletic evolution, and positive or negative selection), and that at least three different functions might be useful. The proposed hit region identification functions that do not benefit from the prior knowledge (i.e., carcinogenicity or invasivity of the involved organisms) can provide equivalent results than the existing functions that take advantage of such a prior knowledge. Using the new algorithm, we examined the
Neisseria meningitidis
FrpB gene product for invasivity and immunologic activity, and human papilloma virus (HPV) E6 oncoprotein for carcinogenicity, and confirmed some well-known molecular features, including surface exposed loops for
N. meningitidis
and PDZ domain for HPV.
Sadri, Javad; Diallo, Abdoulaye Banire; Blanchette, Mathieu
Predicting site-specific human selective pressure using evolutionary signatures Article de journal
Dans: Bioinformatics, vol. 27, no 13, p. i266–i274, 2011, ISSN: 1367-4811, 1367-4803.
@article{sadri_predicting_2011,
title = {Predicting site-specific human selective pressure using evolutionary signatures},
author = {Javad Sadri and Abdoulaye Banire Diallo and Mathieu Blanchette},
url = {https://academic.oup.com/bioinformatics/article/27/13/i266/182309},
doi = {10.1093/bioinformatics/btr241},
issn = {1367-4811, 1367-4803},
year = {2011},
date = {2011-07-01},
urldate = {2024-04-30},
journal = {Bioinformatics},
volume = {27},
number = {13},
pages = {i266\textendashi274},
abstract = {Abstract
Motivation: The identification of non-coding functional regions of the human genome remains one of the main challenges of genomics. By observing how a given region evolved over time, one can detect signs of negative or positive selection hinting that the region may be functional. With the quickly increasing number of vertebrate genomes to compare with our own, this type of approach is set to become extremely powerful, provided the right analytical tools are available.
Results: A large number of approaches have been proposed to measure signs of past selective pressure, usually in the form of reduced mutation rate. Here, we propose a radically different approach to the detection of non-coding functional region: instead of measuring past evolutionary rates, we build a machine learning classifier to predict current substitution rates in human based on the inferred evolutionary events that affected the region during vertebrate evolution. We show that different types of evolutionary events, occurring along different branches of the phylogenetic tree, bring very different amounts of information. We propose a number of simple machine learning classifiers and show that a Support-Vector Machine (SVM) predictor clearly outperforms existing tools at predicting human non-coding functional sites. Comparison to external evidences of selection and regulatory function confirms that these SVM predictions are more accurate than those of other approaches.
Availability: The predictor and predictions made are available at http://www.mcb.mcgill.ca/textasciitildeblanchem/sadri. Contact: blanchem@mcb.mcgill.ca},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Motivation: The identification of non-coding functional regions of the human genome remains one of the main challenges of genomics. By observing how a given region evolved over time, one can detect signs of negative or positive selection hinting that the region may be functional. With the quickly increasing number of vertebrate genomes to compare with our own, this type of approach is set to become extremely powerful, provided the right analytical tools are available.
Results: A large number of approaches have been proposed to measure signs of past selective pressure, usually in the form of reduced mutation rate. Here, we propose a radically different approach to the detection of non-coding functional region: instead of measuring past evolutionary rates, we build a machine learning classifier to predict current substitution rates in human based on the inferred evolutionary events that affected the region during vertebrate evolution. We show that different types of evolutionary events, occurring along different branches of the phylogenetic tree, bring very different amounts of information. We propose a number of simple machine learning classifiers and show that a Support-Vector Machine (SVM) predictor clearly outperforms existing tools at predicting human non-coding functional sites. Comparison to external evidences of selection and regulatory function confirms that these SVM predictions are more accurate than those of other approaches.
Availability: The predictor and predictions made are available at http://www.mcb.mcgill.ca/textasciitildeblanchem/sadri. Contact: blanchem@mcb.mcgill.ca
Horvath, Julie E.; Sheedy, Christina B.; Merrett, Stephanie L.; Diallo, Abdoulaye Banire; Swofford, David L.; Program, Nisc Comparative Sequencing; Green, Eric D.; Willard, Huntington F.
Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate textitXIST locus Article de journal
Dans: Genome Research, vol. 21, no 6, p. 850–862, 2011, ISSN: 1088-9051.
@article{horvath_comparative_2011,
title = {Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate textitXIST locus},
author = {Julie E. Horvath and Christina B. Sheedy and Stephanie L. Merrett and Abdoulaye Banire Diallo and David L. Swofford and Nisc Comparative Sequencing Program and Eric D. Green and Huntington F. Willard},
url = {http://genome.cshlp.org/lookup/doi/10.1101/gr.111849.110},
doi = {10.1101/gr.111849.110},
issn = {1088-9051},
year = {2011},
date = {2011-06-01},
urldate = {2024-04-30},
journal = {Genome Research},
volume = {21},
number = {6},
pages = {850\textendash862},
abstract = {Here we provide a detailed comparative analysis across the candidate X-Inactivation Center (XIC) region and the
XIST
locus in the genomes of six primates and three mammalian outgroup species. Since lemurs and other strepsirrhine primates represent the sister lineage to all other primates, this analysis focuses on lemurs to reconstruct the ancestral primate sequences and to gain insight into the evolution of this region and the genes within it. This comparative evolutionary genomics approach reveals significant expansion in genomic size across the XIC region in higher primates, with minimal size alterations across the
XIST
locus itself. Reconstructed primate ancestral XIC sequences show that the most dramatic changes during the past 80 million years occurred between the ancestral primate and the lineage leading to Old World monkeys. In contrast, the
XIST
locus compared between human and the primate ancestor does not indicate any dramatic changes to exons or
XIST
-specific repeats; rather, evolution of this locus reflects small incremental changes in overall sequence identity and short repeat insertions. While this comparative analysis reinforces that the region around
XIST
has been subject to significant genomic change, even among primates, our data suggest that evolution of the
XIST
sequences themselves represents only small lineage-specific changes across the past 80 million years.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
XIST
locus in the genomes of six primates and three mammalian outgroup species. Since lemurs and other strepsirrhine primates represent the sister lineage to all other primates, this analysis focuses on lemurs to reconstruct the ancestral primate sequences and to gain insight into the evolution of this region and the genes within it. This comparative evolutionary genomics approach reveals significant expansion in genomic size across the XIC region in higher primates, with minimal size alterations across the
XIST
locus itself. Reconstructed primate ancestral XIC sequences show that the most dramatic changes during the past 80 million years occurred between the ancestral primate and the lineage leading to Old World monkeys. In contrast, the
XIST
locus compared between human and the primate ancestor does not indicate any dramatic changes to exons or
XIST
-specific repeats; rather, evolution of this locus reflects small incremental changes in overall sequence identity and short repeat insertions. While this comparative analysis reinforces that the region around
XIST
has been subject to significant genomic change, even among primates, our data suggest that evolution of the
XIST
sequences themselves represents only small lineage-specific changes across the past 80 million years.
Diallo, Abdoulaye Baniré; Badescu, Dunarel; Blanchette, Mathieu; Makarenkov, Vladimir
Classification of the Human Papilloma Viruses Section de livre
Dans: Fichet, Bernard; Piccolo, Domenico; Verde, Rosanna; Vichi, Maurizio (Ed.): Classification and Multivariate Analysis for Complex Data Structures, p. 457–464, Springer Berlin Heidelberg, Berlin, Heidelberg, 2011, ISBN: 9783642133114 9783642133121.
@incollection{fichet_classification_2011,
title = {Classification of the Human Papilloma Viruses},
author = {Abdoulaye Banir\'{e} Diallo and Dunarel Badescu and Mathieu Blanchette and Vladimir Makarenkov},
editor = {Bernard Fichet and Domenico Piccolo and Rosanna Verde and Maurizio Vichi},
url = {https://link.springer.com/10.1007/978-3-642-13312-1_48},
doi = {10.1007/978-3-642-13312-1_48},
isbn = {9783642133114 9783642133121},
year = {2011},
date = {2011-01-01},
urldate = {2024-04-30},
booktitle = {Classification and Multivariate Analysis for Complex Data Structures},
pages = {457\textendash464},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Fichet, Bernard; Piccolo, Domenico; Verde, Rosanna; Vichi, Maurizio (Ed.)
Classification and Multivariate Analysis for Complex Data Structures Ouvrage
Springer Berlin Heidelberg, Berlin, Heidelberg, 2011, ISBN: 9783642133114 9783642133121.
@book{fichet_classification_2011-1,
title = {Classification and Multivariate Analysis for Complex Data Structures},
editor = {Bernard Fichet and Domenico Piccolo and Rosanna Verde and Maurizio Vichi},
url = {https://link.springer.com/10.1007/978-3-642-13312-1},
doi = {10.1007/978-3-642-13312-1},
isbn = {9783642133114 9783642133121},
year = {2011},
date = {2011-01-01},
urldate = {2024-04-30},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
series = {Studies in Classification, Data Analysis, and Knowledge Organization},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
2010
Diallo, Abdoulaye Banire; Makarenkov, Vladimir; Blanchette, Mathieu
Ancestors 1.0: a web server for ancestral sequence reconstruction Article de journal
Dans: Bioinformatics, vol. 26, no 1, p. 130–131, 2010, ISSN: 1367-4811, 1367-4803.
@article{diallo_ancestors_2010,
title = {Ancestors 1.0: a web server for ancestral sequence reconstruction},
author = {Abdoulaye Banire Diallo and Vladimir Makarenkov and Mathieu Blanchette},
url = {https://academic.oup.com/bioinformatics/article/26/1/130/181288},
doi = {10.1093/bioinformatics/btp600},
issn = {1367-4811, 1367-4803},
year = {2010},
date = {2010-01-01},
urldate = {2024-04-30},
journal = {Bioinformatics},
volume = {26},
number = {1},
pages = {130\textendash131},
abstract = {Abstract
Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.
Availability: The Ancestors 1.0 is available at http://ancestors.bioinfo.uqam.ca/ancestorWeb/. Contact: diallo.abdoulaye@uqam.ca},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Summary: The computational inference of ancestral genomes consists of five difficult steps: identifying syntenic regions, inferring ancestral arrangement of syntenic regions, aligning multiple sequences, reconstructing the insertion and deletion history and finally inferring substitutions. Each of these steps have received lot of attention in the past years. However, there currently exists no framework that integrates all of the different steps in an easy workflow. Here, we introduce Ancestors 1.0, a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. It implements several alignment algorithms, an indel maximum likelihood solver and a context-dependent maximum likelihood substitution inference algorithm. The results presented by the server include the posterior probabilities for the last two steps of the ancestral genome reconstruction and the expected error rate of each ancestral base prediction.
Availability: The Ancestors 1.0 is available at http://ancestors.bioinfo.uqam.ca/ancestorWeb/. Contact: diallo.abdoulaye@uqam.ca
Badescu, Dunarel; Diallo, Abdoulaye Baniré; Makarenkov, Vladimir
Identification of Specific Genomic Regions Responsible for the Invasivity of Neisseria Meningitidis Section de livre
Dans: Locarek-Junge, Hermann; Weihs, Claus (Ed.): Classification as a Tool for Research, p. 491–499, Springer Berlin Heidelberg, Berlin, Heidelberg, 2010, ISBN: 9783642107443 9783642107450.
@incollection{locarek-junge_identification_2010,
title = {Identification of Specific Genomic Regions Responsible for the Invasivity of Neisseria Meningitidis},
author = {Dunarel Badescu and Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov},
editor = {Hermann Locarek-Junge and Claus Weihs},
url = {https://link.springer.com/10.1007/978-3-642-10745-0_53},
doi = {10.1007/978-3-642-10745-0_53},
isbn = {9783642107443 9783642107450},
year = {2010},
date = {2010-01-01},
urldate = {2024-04-30},
booktitle = {Classification as a Tool for Research},
pages = {491\textendash499},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2009
Diallo, Abdoulaye Baniré; Badescu, Dunarel; Blanchette, Mathieu; Makarenkov, Vladimir
A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses Article de journal
Dans: Journal of Computational Biology, vol. 16, no 10, p. 1461–1473, 2009, ISSN: 1066-5277, 1557-8666.
@article{diallo_whole_2009,
title = {A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses},
author = {Abdoulaye Banir\'{e} Diallo and Dunarel Badescu and Mathieu Blanchette and Vladimir Makarenkov},
url = {http://www.liebertpub.com/doi/10.1089/cmb.2009.0091},
doi = {10.1089/cmb.2009.0091},
issn = {1066-5277, 1557-8666},
year = {2009},
date = {2009-10-01},
urldate = {2024-04-30},
journal = {Journal of Computational Biology},
volume = {16},
number = {10},
pages = {1461\textendash1473},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Diallo, Abdoulaye
2009.
@misc{diallo_inference_2009,
title = {Inference of insertion and deletion scenarios for ancestral genome reconstruction and phylogenetic analyses: algorithms and biological applications},
author = {Abdoulaye Diallo},
url = {https://escholarship.mcgill.ca/concern/theses/xd07gv166},
year = {2009},
date = {2009-01-01},
urldate = {2024-04-30},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
2008
Blanchette, Mathauieu; Diallo, Abdoulaye Baniré; Green, Eric D.; Miller, Webb; Haussler, David
Computational Reconstruction of Ancestral DNA Sequences Section de livre
Dans: Walker, John M.; Murphy, William J. (Ed.): Phylogenomics, vol. 422, p. 171–184, Humana Press, Totowa, NJ, 2008, ISBN: 9781588297648 9781597455817.
@incollection{walker_computational_2008,
title = {Computational Reconstruction of Ancestral DNA Sequences},
author = {Mathauieu Blanchette and Abdoulaye Banir\'{e} Diallo and Eric D. Green and Webb Miller and David Haussler},
editor = {John M. Walker and William J. Murphy},
url = {http://link.springer.com/10.1007/978-1-59745-581-7_11},
doi = {10.1007/978-1-59745-581-7_11},
isbn = {9781588297648 9781597455817},
year = {2008},
date = {2008-01-01},
urldate = {2024-04-30},
booktitle = {Phylogenomics},
volume = {422},
pages = {171\textendash184},
publisher = {Humana Press},
address = {Totowa, NJ},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Badescu, Dunarel; Diallo, Abdoulaye Baniré; Blanchette, Mathieu; Makarenkov, Vladimir
An Evolutionary Study of the Human Papillomavirus Genomes Section de livre
Dans: Nelson, Craig E.; Vialette, Stéphane (Ed.): Comparative Genomics, vol. 5267, p. 128–142, Springer Berlin Heidelberg, Berlin, Heidelberg, 2008, ISBN: 9783540879886 9783540879893.
@incollection{nelson_evolutionary_2008,
title = {An Evolutionary Study of the Human Papillomavirus Genomes},
author = {Dunarel Badescu and Abdoulaye Banir\'{e} Diallo and Mathieu Blanchette and Vladimir Makarenkov},
editor = {Craig E. Nelson and St\'{e}phane Vialette},
url = {http://link.springer.com/10.1007/978-3-540-87989-3_10},
doi = {10.1007/978-3-540-87989-3_10},
isbn = {9783540879886 9783540879893},
year = {2008},
date = {2008-01-01},
urldate = {2024-04-30},
booktitle = {Comparative Genomics},
volume = {5267},
pages = {128\textendash142},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2007
Diallo, Abdoulaye Banire; Makarenkov, Vladimir; Blanchette, Mathieu
Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem Article de journal
Dans: Journal of Computational Biology, vol. 14, no 4, p. 446–461, 2007, ISSN: 1066-5277, 1557-8666.
@article{diallo_exact_2007,
title = {Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem},
author = {Abdoulaye Banire Diallo and Vladimir Makarenkov and Mathieu Blanchette},
url = {http://www.liebertpub.com/doi/10.1089/cmb.2007.A006},
doi = {10.1089/cmb.2007.A006},
issn = {1066-5277, 1557-8666},
year = {2007},
date = {2007-05-01},
urldate = {2024-04-30},
journal = {Journal of Computational Biology},
volume = {14},
number = {4},
pages = {446\textendash461},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2006
Diallo, Abdoulaye Baniré; Makarenkov, Vladimir; Blanchette, Mathieu
Finding Maximum Likelihood Indel Scenarios Section de livre
Dans: Hutchison, David; Kanade, Takeo; Kittler, Josef; Kleinberg, Jon M.; Mattern, Friedemann; Mitchell, John C.; Naor, Moni; Nierstrasz, Oscar; Rangan, C. Pandu; Steffen, Bernhard; Sudan, Madhu; Terzopoulos, Demetri; Tygar, Dough; Vardi, Moshe Y.; Weikum, Gerhard; Bourque, Guillaume; El-Mabrouk, Nadia (Ed.): Comparative Genomics, vol. 4205, p. 171–185, Springer Berlin Heidelberg, Berlin, Heidelberg, 2006, ISBN: 9783540445296 9783540445302.
@incollection{hutchison_finding_2006,
title = {Finding Maximum Likelihood Indel Scenarios},
author = {Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov and Mathieu Blanchette},
editor = {David Hutchison and Takeo Kanade and Josef Kittler and Jon M. Kleinberg and Friedemann Mattern and John C. Mitchell and Moni Naor and Oscar Nierstrasz and C. Pandu Rangan and Bernhard Steffen and Madhu Sudan and Demetri Terzopoulos and Dough Tygar and Moshe Y. Vardi and Gerhard Weikum and Guillaume Bourque and Nadia El-Mabrouk},
url = {http://link.springer.com/10.1007/11864127_14},
doi = {10.1007/11864127_14},
isbn = {9783540445296 9783540445302},
year = {2006},
date = {2006-01-01},
urldate = {2024-04-30},
booktitle = {Comparative Genomics},
volume = {4205},
pages = {171\textendash185},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
Diallo, Abdoulaye Baniré; Makarenkov, Vladimir; Blanchette, Mathieu; Lapointe, François-Joseph
A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model Section de livre
Dans: Batagelj, Vladimir; Bock, Hans-Hermann; Ferligoj, Anuška; Žiberna, Aleš (Ed.): Data Science and Classification, p. 333–340, Springer Berlin Heidelberg, 2006, ISBN: 9783540344155.
@incollection{batagelj_new_2006,
title = {A New Efficient Method for Assessing Missing Nucleotides in DNA Sequences in the Framework of a Generic Evolutionary Model},
author = {Abdoulaye Banir\'{e} Diallo and Vladimir Makarenkov and Mathieu Blanchette and Fran\c{c}ois-Joseph Lapointe},
editor = {Vladimir Batagelj and Hans-Hermann Bock and Anu\v{s}ka Ferligoj and Ale\v{s} \v{Z}iberna},
url = {http://link.springer.com/10.1007/3-540-34416-0_36},
doi = {10.1007/3-540-34416-0_36},
isbn = {9783540344155},
year = {2006},
date = {2006-01-01},
urldate = {2024-04-30},
booktitle = {Data Science and Classification},
pages = {333\textendash340},
publisher = {Springer Berlin Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}
2004
Makarenkov, Vladimir; Boc, Alix; Diallo, Abdoulaye Baniré
Determining Horizontal Gene Transfers in Species Classification: Unique Scenario Section de livre
Dans: Banks, David; McMorris, Frederick R.; Arabie, Phipps; Gaul, Wolfgang (Ed.): Classification, Clustering, and Data Mining Applications, p. 439–446, Springer Berlin Heidelberg, Berlin, Heidelberg, 2004, ISBN: 9783540220145 9783642171031.
@incollection{banks_determining_2004,
title = {Determining Horizontal Gene Transfers in Species Classification: Unique Scenario},
author = {Vladimir Makarenkov and Alix Boc and Abdoulaye Banir\'{e} Diallo},
editor = {David Banks and Frederick R. McMorris and Phipps Arabie and Wolfgang Gaul},
url = {http://link.springer.com/10.1007/978-3-642-17103-1_41},
doi = {10.1007/978-3-642-17103-1_41},
isbn = {9783540220145 9783642171031},
year = {2004},
date = {2004-01-01},
urldate = {2024-04-30},
booktitle = {Classification, Clustering, and Data Mining Applications},
pages = {439\textendash446},
publisher = {Springer Berlin Heidelberg},
address = {Berlin, Heidelberg},
keywords = {},
pubstate = {published},
tppubtype = {incollection}
}