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2. A human-curated annotation of the Candida albicans genome.

Author

Braun, Burkhard R, van Het Hoog, Marco, d'Enfert, Christophe, Martchenko, Mikhail, Dungan, Jan, Kuo, Alan, Inglis, Diane O, Uhl, M Andrew, Hogues, Hervé, Berriman, Matthew, Lorenz, Michael, Levitin, Anastasia, Oberholzer, Ursula, Bachewich, Catherine, Harcus, Doreen, Marcil, Anne, Dignard, Daniel, Iouk, Tatiana, Zito, Rosa, Frangeul, Lionel, Tekaia, Fredj, Rutherford, Kim, Wang, Edwin, Munro, Carol A, Bates, Steve, Gow, Neil A, Hoyer, Lois L, Köhler, Gerwald, Morschhäuser, Joachim, Newport, George, Znaidi, Sadri, Raymond, Martine, Turcotte, Bernard, Sherlock, Gavin, Costanzo, Maria, Ihmels, Jan, Berman, Judith, Sanglard, Dominique, Agabian, Nina, Mitchell, Aaron P, Johnson, Alexander D, Whiteway, Malcolm, and Nantel, André

Subjects
Genetics, Developmental Biology
Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Published
2005

5. Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities: Fostering a Culture of Critical Capacities to Read, Write, Communicate and Engagein Rigorous Scientific Exchanges

Author

Boudabous, Abdellatif, Tekaia, Fredj, Université de Tunis El Manar (UTM), Institut Pasteur [Paris], and The authors acknowledge the help and support of Prof. Fethi Sellaouti, President of the University Tunis El Manar and Prof. Hechmi Louzir, General Director of the Institut Pasteur de Tunis, Tunisia, that allowed the opportunity to set up this course. The authors are thankful for the Tunisian 'Direction Générale de la Recherche Scientifique, DGRS,' the 'Institut Français de Tunisie, IFT,' the 'Agence Universitaire de la Fran- cophonie, AUF,' Jean Luc Souciet, Tom Kingsnorth and the 'Federation of European Biochemical Societies, FEBS' for their financial contributions to the organization of the courses. The authors thank Marc Jouan and Marianne Luca-Hourani, from the Department of International Aairs— Institut Pasteur International Network for their grants contribution to two participants. The authors are grateful to Andrew Moore, Edouard Yeramian and Antonio Lazcano for their comments and feedback on the manuscript.

Subjects
Bioinformatics, communication, capacity building, [SDV]Life Sciences [q-bio], [SHS.EDU]Humanities and Social Sciences/Education, preparing and presenting reviews Scientific Area: Scientific practice, sharing ideas, Genomics, preparing and presenting reviews, Education, scientific literature follow uo, scientific literature follow up, analytical skills, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Science education
Abstract

Publié dans BioEssays, 2020, 42(10), 2000134; International audience; Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1-day lab meeting in the framework of two previously organized 3-month courses on "Bioinformatics and Genome Analyses". The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self-confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses. Lab meetings are at the heart of scientific life because they provide an exceptional environment for developing skills in team work, networking, exchange on research advances and for enhancing self-confidence and career-building by offering young researchers opportunities to learn how to 1) prepare and present personal research findings ; 2) select and discuss challenging papers ; 3) develop and hone analytical skills; 4) practice communication skills. We adapted this concept by incorporating a weekly 1-day lab meeting in the organization of two 3-month "Bioinformat-ics and Genome Analyses" courses [1] that we organized at the Institut Pasteur Tu-nis, Tunisia. The course was intended for about twenty selected young Ph.D. students and researchers with backgrounds in Biology , Mathematics, Statistics or Computer Science. It was focused on topics related to bioinformatics, comparative genomics, metagenomics, genome variant analyses and programming in a Unix environment. In order to foster the participants' involvement in the lab meeting activities, each participant had to prepare a synthetic review based on some selected bib-liographic resources. This "bibliographic project" constituted a significant component of the course outcome, and had to be formally presented at the end of the course. For that purpose, a large number of quality published papers encompassing most of the course topics were specifically collected and passed to the participants. These documents helped the participants to follow the course program and to select adequate papers for their respective projects. Central activities during lab meetings included work toward preparation of the different projects, follow-up of recent scientific literature, critical reading of papers, review preparation, and presentation, as well as idea-sharing through discussion. Figure 1 shows the steps that we followed in the development of activities. Four main operational objectives constituted the backbone of the procedure implementing these activities 1) Training on reading scientific literature; 2) Preparation of oral presentation and synthetic reviews; 3) Organizing and leading lab meetings; 4) Final review presentation and evaluation. In the following we develop the content of these activities and introduce their implementation in the context of the course program.

Published
2020

6. Protection against Mycobacterium ulcerans lesion development by exposure to aquatic insect saliva

Author

Marsollier, Laurent, Deniaux, Estelle, Brodin, Priscille, Marot, Agnes, Wondje, Christelle Mbondji, Saint-Andre, Jean-Paul, Chauty, Annick, Johnson, Christian, Tekaia, Fredj, Yeramian, Edouard, Legras, Pierre, Carbonnelle, Bernard, Reysset, Gilles, Eyangoh, Sara, Milon, Genevieve, Cole, Stewart T., and Aubry, Jacques

Subjects
Mycobacterial infections -- Prevention, Skin -- Ulcers, Skin -- Prevention, West Africa -- Health aspects
Abstract

ABSTRACT Background Buruli ulcer is a severe human skin disease caused by Mycobacterium ulcerans. This disease is primarily diagnosed in West Africa with increasing incidence. Antimycobacterial drug therapy is relatively [...]

Published
2007

7. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., Pain, Arnab, Anderson, Michael J., Wortman, Jennifer R., Kim, H. Stanley, Arroyo, Javier, Berriman, Matthew, Abe, Keietsu, Archer, David B., Bermejo, Clara, Bennett, Joan, Bowyer, Paul, Chen, Dan, Collins, Matthew, Coulsen, Richard, Davies, Robert, Dyer, Paul S., Farman, Mark, Fedorova, Nadia, Fedorova, Natalie, Feldblyum, Tamara V., Fischer, Reinhard, Fosker, Nigel, Fraser, Audrey, Garcia, Jose L., Garcia, Maria J., Goble, Arlette, Goldman, Gustavo H., Gomi, Katsuya, Griffith-Jones, Sam, Gwilliam, Ryan, Haas, Brian, Haas, Hubertus, Harris, David, Horiuchi, H., Huang, Jiaqi, Humphray, Sean, Jimenez, Javier, Keller, Nancy, Khouri, Hoda, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Konzack, Sven, Kulkarni, Resham, Kumagai, Toshitaka, Lafton, Anne, Latge, Jean-Paul, Li, Weixi, Lord, Angela, Lu, Charles, Majoros, William H., May, Gregory S., Miller, Bruce L., Mohamoud, Yasmin, Molina, Maria, Monod, Michel, Mouyna, Isabelle, Mulligan, Stephanie, Murphy, Lee, O'Neil, Susan, Paulsen, Ian, Penalva, Miguel A., Pertea, Mihaela, Price, Claire, Pritchard, Bethan L., Quail, Michael A., Rabbinowitsch, Ester, Rawlins, Neil, Rajandream, Marie-Adele, Reichard, Utz, Renauld, Hubert, Robson, Geoffrey D., de Cordoba, Santiago Rodriguez, Rodriguez-Pena, Jose M., Ronning, Catherine M., Rutter, Simon, Salzberg, Steven L., Sanchez, Miguel, Sanchez-Ferrero, Juan C., Saunders, David, Seeger, Kathy, Squares, Rob, Squares, Steven, Takeuchi, Michio, Tekaia, Fredj, Turner, Geoffrey, de Aldana, Carlos R. Vazquez, Weidman, Janice, White, Owen, Woodward, John, Yu, Jae-Hyuk, Fraser, Claire, Galagan, James E., Asai, Kiyoshi, Machida, Masayuki, Hall, Neil, Barrell, Bart, and Denning, David W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): William C. Nierman (corresponding author) [1]; Arnab Pain [2]; Michael J. Anderson [3]; Jennifer R. Wortman [1]; H. Stanley Kim [1]; Javier Arroyo [4]; Matthew Berriman [2]; Keietsu Abe [...]

Published
2005
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8. Genome evolution in yeasts

Author

Dujon, Bernard, Sherman, David, Fischer, Gilles, Durrens, Pascal, Casaregola, Serge, Lafontaine, Ingrid, de Montigny, Jacky, Marck, Christian, Neuveglise, Cecile, Talla, Emmanuel, Goffard, Nicolas, Frangeul, Lionel, Aigle, Michel, Anthouard, Veronique, Babour, Anna, Barbe, Valerie, Barnay, Stephanie, Blanchin, Sylvie, Beckerich, Jean-Marie, Beyne, Emmanuelle, Bleykasten, Claudine, Boisrame, Anita, Boyer, Jeanne, Cattolico, Laurence, Confanioleri, Fabrice, de Daruvar, Antoine, Despons, Laurence, Fabre, Emmanuelle, Fairhead, Cecile, Ferry-Dumazet, Helene, Groppi, Alexis, Hantraye, Florence, Hennequin, Christophe, Jauniaux, Nicolas, Joyet, Philippe, Kachouri, Rym, Kerrest, Alix, Koszul, Romain, Lemaire, Marc, Lesur, Isabelle, Ma, Laurence, Muller, Heloise, Nicaud, Jean-Marc, Nikolski, Macha, Oztas, Sophie, Ozier-Kalogeropoulos, Odile, Pellenz, Stefan, Potier, Serge, Richard, Guy-Franck, Straub, Marie-Laure, Suleau, Audrey, Swennen, Dominique, Tekaia, Fredj, Wesolowski-Louvel, Micheline, Westhof, Eric, Wirth, Benedicte, Zeniou-Meyer, Maria, Zivanovic, Ivan, Bolotin-Fukuhara, Monique, Thierry, Agnes, Bouchier, Christiane, Caudron, Bernard, Scarpelli, Claude, Gaillardin, Claude, Weissenbach, Jean, Wincker, Patrick, and Souciet, Jean-Luc

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Bernard Dujon (corresponding author) [1]; David Sherman [5, 6]; Gilles Fischer [1]; Pascal Durrens [6, 7]; Serge Casaregola [8]; Ingrid Lafontaine [1]; Jacky de Montigny [9]; Christian Marck [10]; [...]

Published
2004
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15. Evolution of proteomes: fundamental signatures and global trends in amino acid compositions

Author

Yeramian Edouard and Tekaia Fredj

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level. Results In this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment. Conclusion A simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.

Published
2006
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16. A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

Author

Brino Laurent, Dujon Bernard, Tekaia Fredj, and Talla Emmanuel

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Numerous DNA microarray hybridization experiments have been performed in yeast over the last years using either synthetic oligonucleotides or PCR-amplified coding sequences as probes. The design and quality of the microarray probes are of critical importance for hybridization experiments as well as subsequent analysis of the data. Results We present here a novel design of Saccharomyces cerevisiae microarrays based on a refined annotation of the genome and with the aim of reducing cross-hybridization between related sequences. An effort was made to design probes of similar lengths, preferably located in the 3'-end of reading frames. The sequence of each gene was compared against the entire yeast genome and optimal sub-segments giving no predicted cross-hybridization were selected. A total of 5660 novel probes (more than 97% of the yeast genes) were designed. For the remaining 143 genes, cross-hybridization was unavoidable. Using a set of 18 deletant strains, we have experimentally validated our cross-hybridization procedure. Sensitivity, reproducibility and dynamic range of these new microarrays have been measured. Based on this experience, we have written a novel program to design long oligonucleotides for microarray hybridizations of complete genome sequences. Conclusions A validated procedure to predict cross-hybridization in microarray probe design was defined in this work. Subsequently, a novel Saccharomyces cerevisiae microarray (which minimizes cross-hybridization) was designed and constructed. Arrays are available at Eurogentec S. A. Finally, we propose a novel design program, OliD, which allows automatic oligonucleotide design for microarrays. The OliD program is available from authors.

Published
2003
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18. Genomic Exploration of the Hemiascomycetous Yeasts: 21. Comparative functional classification of genes

Author

Gaillardin, Claude, Duchateau-Nguyen, Guillemette, Tekaia, Fredj, Llorente, Bertrand, Casaregola, Serge, Toffano-Nioche, Claire, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, de Montigny, Jacky, Dujon, Bernard, Durrens, Pascal, Lépingle, Andrée, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Termier, Michel, Wésolowski-Louvel, Micheline, Wincker, Patrick, Souciet, Jean-Luc, and Weissenbach, Jean

Published
2000
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19. Genomic Exploration of the Hemiascomycetous Yeasts: 19. Ascomycetes-specific genes

Author

Malpertuy, Alain, Tekaia, Fredj, Casarégola, Serge, Aigle, Michel, Artiguenave, Francois, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, de Montigny, Jacky, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Potier, Serge, Saurin, William, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Dujon, Bernard

Published
2000
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20. Genomic Exploration of the Hemiascomycetous Yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

Author

Llorente, Bertrand, Durrens, Pascal, Malpertuy, Alain, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, Dujon, Bernard, de Montigny, Jacky, Lépingle, Andrée, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Gaillardin, Claude

Published
2000
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21. Genomic Exploration of the Hemiascomycetous Yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae

Author

Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, de Montigny, Jacky, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, Weissenbach, Jean, Souciet, Jean-Luc, and Dujon, Bernard

Published
2000
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23. Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

Author

Tekaia, Fredj, Blandin, Gaëlle, Malpertuy, Alain, Llorente, Bertrand, Durrens, Pascal, Toffano-Nioche, Claire, Ozier-Kalogeropoulos, Odile, Bon, Elisabeth, Gaillardin, Claude, Aigle, Michel, Bolotin-Fukuhara, Monique, Casarégola, Serge, de Montigny, Jacky, Lépingle, Andrée, Neuvéglise, Cécile, Potier, Serge, Souciet, Jean-Luc, Wésolowski-Louvel, Micheline, and Dujon, Bernard

Published
2000
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24. Genomic Exploration of the Hemiascomycetous Yeasts: 1. A set of yeast species for molecular evolution studies

Author

Souciet, Jean-Luc, Aigle, Michel, Artiguenave, François, Blandin, Gaëlle, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Brottier, Philippe, Casaregola, Serge, de Montigny, Jacky, Dujon, Bernard, Durrens, Pascal, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogéropoulos, Odile, Potier, Serge, Saurin, William, Tekaia, Fredj, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Wincker, Patrick, and Weissenbach, Jean

Published
2000
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25. Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited

Author

Blandin, Gaëlle, Durrens, Pascal, Tekaia, Fredj, Aigle, Michel, Bolotin-Fukuhara, Monique, Bon, Elisabeth, Casarégola, Serge, de Montigny, Jacky, Gaillardin, Claude, Lépingle, Andrée, Llorente, Bertrand, Malpertuy, Alain, Neuvéglise, Cécile, Ozier-Kalogeropoulos, Odile, Perrin, Arnaud, Potier, Serge, Souciet, Jean-Luc, Talla, Emmanuel, Toffano-Nioche, Claire, Wésolowski-Louvel, Micheline, Marck, Christian, and Dujon, Bernard

Published
2000
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26. Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities: Fostering a Culture of Critical Capacities to Read, Write, Communicate and Engage in Rigorous Scientific Exchanges.

Author

Boudabous, Abdellatif and Tekaia, Fredj

Subjects
*MEETINGS, *EXCHANGE of publications, *SCIENTIFIC literature, *GENOMICS, *CAREER development
Abstract

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1‐day lab meeting in the framework of two previously organized 3‐month courses on "Bioinformatics and Genome Analyses". The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self‐confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses. [ABSTRACT FROM AUTHOR]

Published
2020
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27. Genome Data Exploration Using Correspondence Analysis

Author

Tekaia, Fredj, Microbiologie structurale - Structural Microbiology (Microb. Struc. (UMR_3528 / U-Pasteur_5)), Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)

Subjects
correspondence analysis, principal component analysis, genome tree, data mining, bioinformatics, high-dimensional data reduction, amino acid composition, shared orthologs, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], joint representation of observations and variables
Abstract

International audience; Recent developments of sequencing technologies that allow the production of massive amounts of genomic and genotyping data have highlighted the need for synthetic data representation and pattern recognition methods that can mine and help discovering biologically meaningful knowledge included in such large data sets. Correspondence analysis (CA) is an exploratory descriptive method designed to analyze two-way data tables, includ-ing some measure of association between rows and columns. It constructs linear combinations of variables, known as factors. CA has been used for decades to study high-dimensional data, and remarkable inferences from large data tables were obtained by reducing the dimensionality to a few orthogonal factors that correspond to the largest amount of variability in the data. Herein, I review CA and highlight its use by considering examples in handling high-dimen-sional data that can be constructed from genomic and genetic studies. Examples in amino acid compositions of large sets of species (viruses, phages, yeast, and fungi) as well as an example related to pairwise shared orthologs in a set of yeast and fungal species, as obtained from their proteome comparisons, are considered. For the first time, results show striking segregations between yeasts and fungi as well as between viruses and phages. Distributions obtained from shared orthologs show clusters of yeast and fungal species corresponding to their phylogenetic relationships. A direct comparison with the principal component analysis method is discussed using a recently published example of genotyping data related to newly discovered traces of an ancient hominid that was compared to modern human populations in the search for ancestral similarities. CA offers more detailed results highlighting links between modern humans and the ancient hominid and their characterizations. Compared to the popular principal component analysis method, CA allows easier and more effective interpretation of results, particularly by the ability of relating individual patterns with their corresponding characteristic variables.

Published
2016
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30. SuperPartitions: Detection and classification of orthologs

Author

Tekaia, Fredj, Yeramian, Edouard, Génétique Moléculaire des Levures, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Bioinformatique Structurale, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur (PTR No 264 and 370), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Evolution, Paralogs, fungi, Conservation profiles, Genomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Clustering
Abstract

International audience; The proper detection of orthologs is crucial for evolutionary studies of genes and species. Despite large efforts to solve this problem the methodological situation appears unsettled to a large extent and the "quest for orthologs" is still an ongoing task in large-scale genome comparisons. Here, we introduce a simple operational framework for the detection of orthologs and their classification. The operational framework relies on well-established principles, optimizing their implementation for the considered purposes, and chaining components in coherent procedures: 1) We take advantage of the efficiency and simplicity of the Reciprocal Best Hit (RBH) detections, remedying (by design) the drawback concerning the limitations in terms of 1:1 detections. The procedure is based on the partitioning of Reciprocal Best Hits, with the further merging of partitions including members of the same paralogous classes ("SuperPartition of Orthologs" (SPOs)). 2) We then resort to the conservation profiles of the obtained clusters, allowing simple detection of SPOs containing duplicated members. Based on accepted evolutionary principles, such members can be further tagged as in-paralogs (co-orthologs) or out-paralogs. The method is illustrated and validated by extensive genomic analyses. The performances of the overall approach are characterized in global terms for three sets of species (Chlamydiae, Mycobacteria, Aspergilli), showing that at least 75% of the sets of orthologs contain at most one protein from a given species. The sets including more than one protein from a given species are shown to contain in-paralogs in proportions varying from 28% to 58%. The characterizations also show that the large majority of SPOs are associated with ancestral motifs, and accordingly not prone to chaining effects that might be triggered by multi-domain proteins. Further the SPO formulation is compared to other similarity based ortholog detection methods. Beyond core common results, significant differences are observed between various methods, which can be accounted for to a large extent on conceptual grounds, relative to the different merging schemes involved. Such comparisons highlight a major advantage of the SPO approach concerning the proper clustering of associated paralogs, which appear to be often dispatched spuriously into distinct orthologous classes. Finally the perspectives for future applications and elaborations of SPO-based compositional analyses are discussed.

Published
2011
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31. Complete DNA Sequence of Kuraishia capsulata Illustrates Novel Genomic Features among Budding Yeasts (Saccharomycotina)

Author

Morales, Lucia, primary, Noel, Benjamin, additional, Porcel, Betina, additional, Marcet-Houben, Marina, additional, Hullo, Marie-Francoise, additional, Sacerdot, Christine, additional, Tekaia, Fredj, additional, Leh-Louis, Véronique, additional, Despons, Laurence, additional, Khanna, Varun, additional, Aury, Jean-Marc, additional, Barbe, Valérie, additional, Couloux, Arnaud, additional, Labadie, Karen, additional, Pelletier, Eric, additional, Souciet, Jean-Luc, additional, Boekhout, Teun, additional, Gabaldon, Toni, additional, Wincker, Patrick, additional, and Dujon, Bernard, additional

Published
2013
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35. Novel transporters from hemiascomycete yeasts.

Author

UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, De Hertogh, Benoît, Talla, Emmanuel, Tekaia, Fredj, Beyne, Emmanuelle, Sherman, David, Baret, Philippe, Dujon, Bernard, Goffeau, André, UCL - AGRO/BAPA - Département de biologie appliquée et des productions agricoles, De Hertogh, Benoît, Talla, Emmanuel, Tekaia, Fredj, Beyne, Emmanuelle, Sherman, David, Baret, Philippe, Dujon, Bernard, and Goffeau, André

Abstract

We screened nearly one thousand random sequenced targets obtained by partial sequencing of 13 hemiascomycete genomes identified by higher amino acid sequence similarity to a non-Saccharomyces cerevisiae protein than to a S. Cerevisiae protein. Among those sequences we have identified 36 novel phylogenetic clusters of putative transporters which, according to the Transport Commission system (TC-DB, 2002; http:// tcdb.ucsd.edu/tcdb), do not belong to acknowledged S. Cerevisiae protein families [De Hertogh et al.: Funct. Integr. Genomics 2002;2:154-170; http://cbi.labri.u-bordeaux.fr/Genolevures]. These novel hemiascomycete transporters comprise 3 channels, 23 secondary transporters, 5 primary transporters and 5 membrane proteins of unknown function.

Published
2003

36. Use of Fine-Needle Aspiration for Diagnosis of Mycobacterium ulcerans Infection

Author

Cassisa, Viviane, primary, Chauty, Annick, additional, Marion, Estelle, additional, Ardant, Marie Françoise, additional, Eyangoh, Sara, additional, Cottin, Jane, additional, Aubry, Jacques, additional, Koussemou, Hugues, additional, Lelièvre, Bénédicte, additional, Férec, Séverine, additional, Tekaia, Fredj, additional, Johnson, Christian, additional, and Marsollier, Laurent, additional

Published
2010
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38. Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., Pain, Arnab, Anderson, Michael J., Wortman, Jennifer R., Kim, H. Stanley, Arroyo, Javier, Berriman, Matthew, Abe, Keietsu, Archer, David B., Bermejo, Clara, Bennett, Joan, Bowyer, Paul, Chen, Dan, Collins, Matthew, Coulsen, Richard, Davies, Robert, Dyer, Paul S., Farman, Mark, Fedorova, Nadia, Fedorova, Natalie, Feldblyum, Tamara V., Fischer, Reinhard, Fosker, Nigel, Fraser, Audrey, Garcia, Jose L., Garcia, Maria J., Goble, Arlette, Goldman, Gustavo H., Gomi, Katsuya, Griffith-Jones, Sam, Gwilliam, Ryan, Haas, Brian, Haas, Hubertus, Harris, David, Horiuchi, H., Huang, Jiaqi, Humphray, Sean, Jimenez, Javier, Keller, Nancy, Khouri, Hoda, Kitamoto, Katsuhiko, Kobayashi, Tetsuo, Konzack, Sven, Kulkarni, Resham, Kumagai, Toshitaka, Lafon, Anne, Latge, Jean-Paul, Li, Weixi, Lord, Angela, Lu, Charles, Majoros, William H., May, Gregory S., Miller, Bruce L., Mohamoud, Yasmin, Molina, Maria, Monod, Michel, Mouyna, Isabelle, Mulligan, Stephanie, Murphy, Lee, O'Neil, Susan, Paulsen, Ian, Penalva, Miguel A., Pertea, Mihaela, Price, Claire, Pritchard, Bethan L., Quail, Michael A., Rabbinowitsch, Ester, Rawlins, Neil, Rajandream, Marie-Adele, Reichard, Utz, Renauld, Hubert, Robson, Geoffrey D., de Cordoba, Santiago Rodriguez, Rodriguez-Pena, Jose M., Ronning, Catherine M., Rutter, Simon, Salzberg, Steven L., Sanchez, Miguel, Sanchez-Ferrero, Juan C., Saunders, David, Seeger, Kathy, Squares, Rob, Squares, Steven, Takeuchi, Michio, Tekaia, Fredj, Turner, Geoffrey, de Aldana, Carlos R. Vazquez, Weidman, Janice, White, Owen, Woodward, John, Yu, Jae-Hyuk, Fraser, Claire, Galagan, James E., Asai, Kiyoshi, Machida, Masayuki, Hall, Neil, Barrell, Bart, and Denning, David W.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): William C. Nierman; Arnab Pain; Michael J. Anderson; Jennifer R. Wortman; H. Stanley Kim; Javier Arroyo; Matthew Berriman; Keietsu Abe; David B. Archer; Clara Bermejo; Joan Bennett; Paul Bowyer; [...]

Published
2006
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39. Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Author

Stinear, Timothy P., primary, Seemann, Torsten, additional, Pidot, Sacha, additional, Frigui, Wafa, additional, Reysset, Gilles, additional, Garnier, Thierry, additional, Meurice, Guillaume, additional, Simon, David, additional, Bouchier, Christiane, additional, Ma, Laurence, additional, Tichit, Magali, additional, Porter, Jessica L., additional, Ryan, Janine, additional, Johnson, Paul D.R., additional, Davies, John K., additional, Jenkin, Grant A., additional, Small, Pamela L.C., additional, Jones, Louis M., additional, Tekaia, Fredj, additional, Laval, Françoise, additional, Daffé, Mamadou, additional, Parkhill, Julian, additional, and Cole, Stewart T., additional

Published
2007
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41. Erratum: Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus

Author

Nierman, William C., primary, Pain, Arnab, additional, Anderson, Michael J., additional, Wortman, Jennifer R., additional, Kim, H. Stanley, additional, Arroyo, Javier, additional, Berriman, Matthew, additional, Abe, Keietsu, additional, Archer, David B., additional, Bermejo, Clara, additional, Bennett, Joan, additional, Bowyer, Paul, additional, Chen, Dan, additional, Collins, Matthew, additional, Coulsen, Richard, additional, Davies, Robert, additional, Dyer, Paul S., additional, Farman, Mark, additional, Fedorova, Nadia, additional, Fedorova, Natalie, additional, Feldblyum, Tamara V., additional, Fischer, Reinhard, additional, Fosker, Nigel, additional, Fraser, Audrey, additional, García, Jose L., additional, García, Maria J., additional, Goble, Arlette, additional, Goldman, Gustavo H., additional, Gomi, Katsuya, additional, Griffith-Jones, Sam, additional, Gwilliam, Ryan, additional, Haas, Brian, additional, Haas, Hubertus, additional, Harris, David, additional, Horiuchi, H., additional, Huang, Jiaqi, additional, Humphray, Sean, additional, Jiménez, Javier, additional, Keller, Nancy, additional, Khouri, Hoda, additional, Kitamoto, Katsuhiko, additional, Kobayashi, Tetsuo, additional, Konzack, Sven, additional, Kulkarni, Resham, additional, Kumagai, Toshitaka, additional, Lafon, Anne, additional, Latgé, Jean-Paul, additional, Li, Weixi, additional, Lord, Angela, additional, Lu, Charles, additional, Majoros, William H., additional, May, Gregory S., additional, Miller, Bruce L., additional, Mohamoud, Yasmin, additional, Molina, Maria, additional, Monod, Michel, additional, Mouyna, Isabelle, additional, Mulligan, Stephanie, additional, Murphy, Lee, additional, O'Neil, Susan, additional, Paulsen, Ian, additional, Peñalva, Miguel A., additional, Pertea, Mihaela, additional, Price, Claire, additional, Pritchard, Bethan L., additional, Quail, Michael A., additional, Rabbinowitsch, Ester, additional, Rawlins, Neil, additional, Rajandream, Marie-Adele, additional, Reichard, Utz, additional, Renauld, Hubert, additional, Robson, Geoffrey D., additional, de Córdoba, Santiago Rodriguez, additional, Rodríguez-Peña, Jose M., additional, Ronning, Catherine M., additional, Rutter, Simon, additional, Salzberg, Steven L., additional, Sanchez, Miguel, additional, Sánchez-Ferrero, Juan C., additional, Saunders, David, additional, Seeger, Kathy, additional, Squares, Rob, additional, Squares, Steven, additional, Takeuchi, Michio, additional, Tekaia, Fredj, additional, Turner, Geoffrey, additional, de Aldana, Carlos R. Vazquez, additional, Weidman, Janice, additional, White, Owen, additional, Woodward, John, additional, Yu, Jae-Hyuk, additional, Fraser, Claire, additional, Galagan, James E., additional, Asai, Kiyoshi, additional, Machida, Masayuki, additional, Hall, Neil, additional, Barrell, Bart, additional, and Denning, David W., additional

Published
2006
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45. Expressed Sequence Tag Analysis of the Human Pathogen Paracoccidioides brasiliensis Yeast Phase: Identification of Putative Homologues of Candida albicans Virulence and Pathogenicity Genes

Author

Goldman, Gustavo H., primary, dos Reis Marques, Everaldo, additional, Duarte Ribeiro, Diógenes Custódio, additional, de Souza Bernardes, Luciano Ângelo, additional, Quiapin, Andréa Carla, additional, Vitorelli, Patrícia Marostica, additional, Savoldi, Marcela, additional, Semighini, Camile P., additional, de Oliveira, Regina C., additional, Nunes, Luiz R., additional, Travassos, Luiz R., additional, Puccia, Rosana, additional, Batista, Wagner L., additional, Ferreira, Leslie Ecker, additional, Moreira, Júlio C., additional, Bogossian, Ana Paula, additional, Tekaia, Fredj, additional, Nobrega, Marina Pasetto, additional, Nobrega, Francisco G., additional, and Goldman, Maria Helena S., additional

Published
2003
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46. Novel Transporters from Hemiascomycete Yeasts

Author

De Hertogh, Benoît, primary, Talla, Emmanuel, additional, Tekaia, Fredj, additional, Beyne, Emmanuelle, additional, Sherman, David, additional, Baret, Philippe V., additional, Dujon, Bernard, additional, and Goffeau, André, additional

Published
2003
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49. The decaying genome ofMycobacterium leprae

Author

EIGLMEIER, KARIN, primary, PARKHILL, JULIAN, additional, HONORÉ, NADINE, additional, GARNIER, THIERRY, additional, TEKAIA, FREDJ, additional, TELENTI, AMALIO, additional, KLATSER, PAUL, additional, JAMES, KEITH D., additional, THOMSON, NICOLAS R., additional, WHEELER, PAUL R., additional, CHURCHER, CAROL, additional, HARRIS, DAVID, additional, MUNGALL, KAREN, additional, BARRELL, BART G., additional, and COLE, STEWART T., additional

Published
2001
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