Molecular Bio-informatics

Roginski, Paul, Anna Grandchamp, Chloé Quignot, and Anne Lopes. 2024. “De Novo Emerged Gene Search in Eukaryotes with DENSE.” Genome Biology and Evolution 16 (8): evae159. https://doi.org/10.1093/gbe/evae159.

Sebastià, C., M. Gallopin, Y. Ramayo-Caldas, J. Estellé, J. Valdés-Hernández, A. Castelló, A. Sánchez, D. Crespo-Piazuelo, and J. M. Folch. 2024. “Gene Co-Expression Network Analysis for Porcine Intramuscular Fatty Acid Composition.” Animal: An International Journal of Animal Bioscience 18 (9): 101259. https://doi.org/10.1016/j.animal.2024.101259.

Nocente, Marina C., Anida Mesihovic Karamitsos, Emilie Drouineau, Manon Soleil, Waad Albawardi, Cécile Dulary, Florence Ribierre, et al. 2024. “CBAF Generates Subnucleosomes That Expand OCT4 Binding and Function beyond DNA Motifs at Enhancers.” Nature Structural & Molecular Biology, July. https://doi.org/10.1038/s41594-024-01344-0.

Xue, Haoliang, Mélina Gallopin, Camille Marchet, Ha N. Nguyen, Yunfeng Wang, Antoine Lainé, Chloé Bessiere, and Daniel Gautheret. 2024. “KaMRaT: A C ++ Toolkit for k-Mer Count Matrix Dimension Reduction.” Bioinformatics (Oxford, England), March, btae090. https://doi.org/10.1093/bioinformatics/btae090.

Rossier, Ombeline, Cécile Labarre, Anne Lopes, Monique Auberdiac, Kevin Tambosco, Daniel Delaruelle, Hakima Abes, et al. 2024. “Genome Sequence of PSonyx, a Singleton Bacteriophage Infecting Corynebacterium Glutamicum.” Microbiology Resource Announcements, January, e0115523. https://doi.org/10.1128/mra.01155-23.

Poinsignon, Thibault, Mélina Gallopin, Pierre Grognet, Fabienne Malagnac, Gaëlle Lelandais, and Pierre Poulain. 2023. “3D Models of Fungal Chromosomes to Enhance Visual Integration of Omics Data.” NAR Genomics and Bioinformatics 5 (4): lqad104. https://doi.org/10.1093/nargab/lqad104.

Barone, M., Y. Ramayo-Caldas, J. Estellé, K. Tambosco, S. Chadi, F. Maillard, M. Gallopin, et al. 2023. “Gut Barrier-Microbiota Imbalances in Early Life Lead to Higher Sensitivity to Inflammation in a Murine Model of C-Section Delivery.” Microbiome 11 (1): 140. https://doi.org/10.1186/s40168-023-01584-0.

Oliveira, Leonor, Nicolas Chevrollier, Jean-Felix Dallery, Richard J. O’Connell, Marc-Henri Lebrun, Muriel Viaud, and Olivier Lespinet. 2023. “CusProSe: A Customizable Protein Annotation Software with an Application to the Prediction of Fungal Secondary Metabolism Genes.” Scientific Reports 13 (1): 1417. https://doi.org/10.1038/s41598-023-27813-y.

Gianfrotta, Coline, Vladimir Reinharz, Olivier Lespinet, Dominique Barth, and Alain Denise. 2022. “On the Predictibility of A-Minor Motifs from Their Local Contexts.” RNA Biology 19 (1): 1208–27. https://doi.org/10.1080/15476286.2022.2144611.

Bastide, Paul, Charlotte Soneson, David B Stern, Olivier Lespinet, and Mélina Gallopin. 2022. “A Phylogenetic Framework to Simulate Synthetic Inter-Species RNA-Seq Data.” Molecular Biology and Evolution, December, msac269. https://doi.org/10.1093/molbev/msac269.

Papadopoulos, Chris, Isabelle Callebaut, Jean-Christophe Gelly, Isabelle Hatin, Olivier Namy, Maxime Renard, Olivier Lespinet, and Anne Lopes. 2021. “Intergenic ORFs as Elementary Structural Modules of de Novo Gene Birth and Protein Evolution.” Genome Research, November. https://doi.org/10.1101/gr.275638.121.

Bacle, Amélie, Pavel Buslaev, Rebeca Garcia-Fandino, Fernando Favela-Rosales, Tiago Mendes Ferreira, Patrick F. J. Fuchs, Ivan Gushchin, et al. 2021. “Inverse Conformational Selection in Lipid-Protein Binding.” Journal of the American Chemical Society 143 (34): 13701–9. https://doi.org/10.1021/jacs.1c05549.

Alpha-Bazin, Béatrice, Aurore Gorlas, Arnaud Lagorce, Damien Joulié, Jean-Baptiste Boyer, Murielle Dutertre, Jean-Charles Gaillard, et al. 2021. “Lysine-Specific Acetylated Proteome from the Archaeon Thermococcus Gammatolerans Reveals the Presence of Acetylated Histones.” Journal of Proteomics 232 (February):104044. https://doi.org/10.1016/j.jprot.2020.104044.

Hadjadj, Djihad, Thomas Denecker, Eva Guérin, Su-Jung Kim, Fabien Fauchereau, Giuseppe Baldacci, Chrystelle Maric, and Jean-Charles Cadoret. 2020. “Efficient, Quick and Easy-to-Use DNA Replication Timing Analysis with START-R Suite.” NAR Genomics and Bioinformatics 2 (2). https://doi.org/10.1093/nargab/lqaa045.

Godat, Emmanuel, Jean-Charles Preiser, Jean-Christophe Aude, and Pierre Kalfon. 2020. “Dynamic Properties of Glucose Complexity during the Course of Critical Illness: A Pilot Study.” Journal of Clinical Monitoring and Computing 34 (2): 361–70. https://doi.org/10.1007/s10877-019-00299-8.

Schweke, Hugo, Marie-Hélène Mucchielli, Sophie Sacquin-Mora, Wanying Bei, and Anne Lopes. 2020. “Protein Interaction Energy Landscapes Are Shaped by Functional and Also Non-Functional Partners.” Journal of Molecular Biology 432 (4): 1183–98. https://doi.org/10.1016/j.jmb.2019.12.047.

Marichal, Laurent, Geraldine Klein, Jean Armengaud, Yves Boulard, Stephane Chedin, Jean Labarre, Serge Pin, Jean-Philippe Renault, and Jean-Christophe Aude. 2020. “Protein Corona Composition of Silica Nanoparticles in Complex Media: Nanoparticle Size Does Not Matter.” Nanomaterials 10 (2): 240. https://doi.org/10.3390/nano10020240.

Pinskaya, Marina, Zohra Saci, Mélina Gallopin, Marc Gabriel, Ha Tn Nguyen, Virginie Firlej, Marc Descrimes, et al. 2019. “Reference-Free Transcriptome Exploration Reveals Novel RNAs for Prostate Cancer Diagnosis.” Life Science Alliance 2 (6): e201900449. https://doi.org/10.26508/lsa.201900449.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, and Pierre Leblond. 2019. “Genome Sequences of 11 Conspecific Streptomyces Sp. Strains.” Microbiology Resource Announcements 8 (38): e00863-19. https://doi.org/10.1128/MRA.00863-19.

Tidjani, Abdoul-Razak, Jean-Noël Lorenzi, Maxime Toussaint, Erwin van Dijk, Delphine Naquin, Olivier Lespinet, Cyril Bontemps, and Pierre Leblond. 2019. “Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.” MBio 10 (5): e01533-19. https://doi.org/10.1128/mBio.01533-19.

Lorenzi, Jean-Noël, Olivier Lespinet, Pierre Leblond, and Annabelle Thibessard. 2019. “Subtelomeres Are Fast-Evolving Regions of the Streptomyces Linear Chromosome.” Microbial Genomics 7 (6). https://doi.org/10.1099/mgen.0.000525.

Marichal, Laurent, Gaël Giraudon--Colas, Fabrice Cousin, Antoine Thill, Jean Labarre, Yves Boulard, Jean-Christophe Aude, Serge Pin, and Jean Philippe Renault. 2019. “Protein–Nanoparticle Interactions: What Are the Protein–Corona Thickness and Organization?” Langmuir 35 (33): 10831–37. https://doi.org/10.1021/acs.langmuir.9b01373.

Zaharia, Alexandra, Bernard Labedan, Christine Froidevaux, and Alain Denise. 2019. “CoMetGeNe: Mining Conserved Neighborhood Patterns in Metabolic and Genomic Contexts.” BMC Bioinformatics 20 (1): 19. https://doi.org/10.1186/s12859-018-2542-2.

Petitalot, Ambre, Elodie Dardillac, Eric Jacquet, Naima Nhiri, Josee Guirouilh-Barbat, Patrick Julien, Isslam Bouazzaoui, et al. 2019. “Combining Homologous Recombination and Phosphopeptide-Binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk.” Molecular Cancer Research 17 (1): 54–69. https://doi.org/10.1158/1541-7786.MCR-17-0357.

Denecker, Thomas, William Durand, Julien Maupetit, Charles Hébert, Jean-Michel Camadro, Pierre Poulain, and Gaëlle Lelandais. 2019. “Pixel: A Content Management Platform for Quantitative Omics Data.” PeerJ 7:e6623. https://doi.org/10.7717/peerj.6623.

Godinho, Lia M., Mehdi El Sadek Fadel, Celine Monniot, Lina Jakutyte, Isabelle Auzat, Audrey Labarde, Karima Djacem, et al. 2018. “The Revisited Genome of Bacillus Subtilis Bacteriophage SPP1.” Viruses-Basel 10 (12): 705. https://doi.org/10.3390/v10120705.

Vicente, Claudia M., Annabelle Thibessard, Jean-Noel Lorenzi, Mabrouka Benhadj, Laurence Hotel, Djamila Gacemi-Kirane, Olivier Lespinet, Pierre Leblond, and Bertrand Aigle. 2018. “Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity.” Antibiotics-Basel 7 (4): 86. https://doi.org/10.3390/antibiotics7040086.

Denecker, Thomas, and Gaëlle Lelandais. 2018. “Empowering the Detection of ChIP-Seq ‘Basic Peaks’ (BPeaks) in Small Eukaryotic Genomes with a Web User-Interactive Interface.” BMC Research Notes 11 (1): 698. https://doi.org/10.1186/s13104-018-3802-y.

Marichal, Laurent, Jean-Philippe Renault, Stéphane Chédin, Gilles Lagniel, Géraldine Klein, Jean-Christophe Aude, Carine Tellier-Lebegue, et al. 2018. “Importance of Post-Translational Modifications in the Interaction of Proteins with Mineral Surfaces: The Case of Arginine Methylation and Silica Surfaces.” Langmuir: The ACS Journal of Surfaces and Colloids 34 (18): 5312–22. https://doi.org/10.1021/acs.langmuir.8b00752.

Reinharz, Vladimir, Antoine Soule, Eric Westhof, Jerome Waldispuhl, and Alain Denise. 2018. “Mining for Recurrent Long-Range Interactions in RNA Structures Reveals Embedded Hierarchies in Network Families.” Nucleic Acids Research 46 (8): 3841–51. https://doi.org/10.1093/nar/gky197.

Abdollahi, Nika, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, et al. 2018. “Meet-U: Educating through Research Immersion.” PLoS Computational Biology 14 (3): e1005992. https://doi.org/10.1371/journal.pcbi.1005992.

Forslund, Kristoffer, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, et al. 2018. “Gearing up to Handle the Mosaic Nature of Life in the Quest for Orthologs.” Bioinformatics 34 (2): 323–29. https://doi.org/10.1093/bioinformatics/btx542.

Benchouaia, Médine, Hugues Ripoche, Mariam Sissoko, Antonin Thiébaut, Jawad Merhej, Thierry Delaveau, Laure Fasseu, et al. 2018. “Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida Glabrata.” Frontiers in Microbiology 9:2689. https://doi.org/10.3389/fmicb.2018.02689.

Henríquez-Castillo, Carlos, Hugo Botebol, Adelaide Mouton, Salvador Ramírez-Flandes, Jean-Claude Lozano, Gaelle Lelandais, Santiago Andrade, Nicole Trefault, Rodrigo De la Iglesia, and François-Yves Bouget. 2018. “Ostreococcus Tauri Luminescent Reporter Lines as Biosensors for Detecting Pollution From Copper-Mine Tailing Effluents in Coastal Environments.” Frontiers in Environmental Science 6. https://doi.org/10.3389/fenvs.2018.00022.

Audoux, Jérôme, Nicolas Philippe, Rayan Chikhi, Mikaël Salson, Mélina Gallopin, Marc Gabriel, Jérémy Le Coz, Emilie Drouineau, Thérèse Commes, and Daniel Gautheret. 2017. “DE-Kupl: Exhaustive Capture of Biological Variation in RNA-Seq Data through k-Mer Decomposition.” Genome Biology 18 (1): 243. https://doi.org/10.1186/s13059-017-1372-2.

Dallery, Jean-Félix, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigné, Isabelle Luyten, Joëlle Amselem, Alexander H. J. Wittenberg, et al. 2017. “Gapless Genome Assembly of Colletotrichum Higginsianum Reveals Chromosome Structure and Association of Transposable Elements with Secondary Metabolite Gene Clusters.” BMC Genomics 18 (1): 667. https://doi.org/10.1186/s12864-017-4083-x.

Boudard, Mélanie, Dominique Barth, Julie Bernauer, Alain Denise, and Johanne Cohen. 2017. “GARN2: Coarse-Grained Prediction of 3D Structure of Large RNA Molecules by Regret Minimization.” Bioinformatics 33 (16): 2479–86. https://doi.org/10.1093/bioinformatics/btx175.

Glatigny, Annie, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin, and Marie-Hélène Mucchielli-Giorgi. 2017. “Development of an in Silico Method for the Identification of Subcomplexes Involved in the Biogenesis of Multiprotein Complexes in Saccharomyces Cerevisiae.” BMC Systems Biology 11 (1): 67. https://doi.org/10.1186/s12918-017-0442-0.

Thiébaut, Antonin, Thierry Delaveau, Médine Benchouaia, Julia Boeri, Mathilde Garcia, Gaëlle Lelandais, and Frédéric Devaux. 2017. “The CCAAT-Binding Complex Controls Respiratory Gene Expression and Iron Homeostasis in Candida Glabrata.” Scientific Reports 7 (1): 3531. https://doi.org/10.1038/s41598-017-03750-5.

Klein, Géraldine, Christelle Mathé, Mathilde Biola-Clier, Stéphanie Devineau, Emilie Drouineau, Elie Hatem, Laurent Marichal, et al. 2016. “RNA-Binding Proteins Are a Major Target of Silica Nanoparticles in Cell Extracts.” Nanotoxicology 10 (10): 1555–64. https://doi.org/10.1080/17435390.2016.1244299.

Hacquard, Stéphane, Barbara Kracher, Kei Hiruma, Philipp C. Münch, Ruben Garrido-Oter, Michael R. Thon, Aaron Weimann, et al. 2016. “Erratum: Survival Trade-Offs in Plant Roots during Colonization by Closely Related Beneficial and Pathogenic Fungi.” Nature Communications 7 (September):13072. https://doi.org/10.1038/ncomms13072.

Yi, Zhou, Marion Manil-Ségalen, Laila Sago, Annie Glatigny, Virginie Redeker, Renaud Legouis, and Marie-Hélène Mucchielli-Giorgi. 2016. “SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. Elegans Autophagic Protein LGG-1.” Journal of Proteome Research 15 (5): 1515–23. https://doi.org/10.1021/acs.jproteome.5b01158.

Hacquard, Stéphane, Barbara Kracher, Kei Hiruma, Philipp C. Münch, Ruben Garrido-Oter, Michael R. Thon, Aaron Weimann, et al. 2016. “Survival Trade-Offs in Plant Roots during Colonization by Closely Related Beneficial and Pathogenic Fungi.” Nature Communications 7 (May):11362. https://doi.org/10.1038/ncomms11362.

Ithurbide, Solenne, Esma Bentchikou, Geneviève Coste, Bruno Bost, Pascale Servant, and Suzanne Sommer. 2015. “Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus Radiodurans Bacterium.” PLoS Genetics 11 (10): e1005636. https://doi.org/10.1371/journal.pgen.1005636.

Gophna, Uri, David M. Kristensen, Yuri I. Wolf, Ovidiu Popa, Christine Drevet, and Eugene V. Koonin. 2015. “No Evidence of Inhibition of Horizontal Gene Transfer by CRISPR-Cas on Evolutionary Timescales.” The ISME Journal 9 (9): 2021–27. https://doi.org/10.1038/ismej.2015.20.

Brancotte, Bryan, Bo Yang, Guillaume Blin, Sarah Cohen-Boulakia, Alain Denise, and Sylvie Hamel. 2015. “Rank Aggregation with Ties: Experiments and Analysis.” Proceedings of the VLDB Endowment 8 (11): 1202–13. https://doi.org/10.14778/2809974.2809982.

Lasserre, J.-P., A. Dautant, R. S. Aiyar, R. Kucharczyk, A. Glatigny, D. Tribouillard-Tanvier, J. Rytka, et al. 2015. “Yeast as a System for Modeling Mitochondrial Disease Mechanisms and Discovering Therapies.” Disease Models & Mechanisms 8 (6): 509–26. https://doi.org/10.1242/dmm.020438.

Boudard, Mélanie, Julie Bernauer, Dominique Barth, Johanne Cohen, and Alain Denise. 2015. “GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.” PloS One 10 (8): e0136444. https://doi.org/10.1371/journal.pone.0136444.