Advanced Search
Display options
Filter resources
Text Availability
Article type
Publication date
Species
Language
Sex
Age
Showing 1 to 12 of 16 entries
Sorted by: Best Match Show Resources per page
MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries.

Frontiers in genetics

Baudry L, Foutel-Rodier T, Thierry A, Koszul R, Marbouty M.
PMID: 31481973
Front Genet. 2019 Aug 20;10:753. doi: 10.3389/fgene.2019.00753. eCollection 2019.

Characterizing the complete genomic structure of complex microbial communities would represent a key step toward the understanding of their diversity, dynamics, and evolution. Current metagenomics approaches aiming at this goal are typically done by analyzing millions of short DNA...

Cite
Baudry L, Foutel-Rodier T, Thierry A, et al. MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries. Front Genet. 2019;10:753doi: 10.3389/fgene.2019.00753.
Baudry, L., Foutel-Rodier, T., Thierry, A., Koszul, R., & Marbouty, M. (2019). MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries. Frontiers in genetics, 10753. https://doi.org/10.3389/fgene.2019.00753
Baudry, Lyam, et al. "MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries." Frontiers in genetics vol. 10 (2019): 753. doi: https://doi.org/10.3389/fgene.2019.00753
Baudry L, Foutel-Rodier T, Thierry A, Koszul R, Marbouty M. MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries. Front Genet. 2019 Aug 20;10:753. doi: 10.3389/fgene.2019.00753. eCollection 2019. PMID: 31481973; PMCID: PMC6710406.
Copy Download .nbib Format: NLM
Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization.

Communications biology

Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM.
PMID: 34331006
Commun Biol. 2021 Jul 30;4(1):940. doi: 10.1038/s42003-021-02480-9.

No abstract available.

Cite
Gauthier J, Boulain H, van Vugt JJFA, et al. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol. 2021;4(1):940doi: 10.1038/s42003-021-02480-9.
Gauthier, J., Boulain, H., van Vugt, J. J. F. A., Baudry, L., Persyn, E., Aury, J. M., Noel, B., Bretaudeau, A., Legeai, F., Warris, S., Chebbi, M. A., Dubreuil, G., Duvic, B., Kremer, N., Gayral, P., Musset, K., Josse, T., Bigot, D., Bressac, C., Moreau, S., Periquet, G., Harry, M., Montagné, N., Boulogne, I., Sabeti-Azad, M., Maïbèche, M., Chertemps, T., Hilliou, F., Siaussat, D., Amselem, J., Luyten, I., Capdevielle-Dulac, C., Labadie, K., Merlin, B. L., Barbe, V., de Boer, J. G., Marbouty, M., Cônsoli, F. L., Dupas, S., Hua-Van, A., Le Goff, G., Bézier, A., Jacquin-Joly, E., Whitfield, J. B., Vet, L. E. M., Smid, H. M., Kaiser, L., Koszul, R., Huguet, E., Herniou, E. A., & Drezen, J. M. (2021). Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Communications biology, 4(1), 940. https://doi.org/10.1038/s42003-021-02480-9
Gauthier, Jérémy, et al. "Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization." Communications biology vol. 4,1 (2021): 940. doi: https://doi.org/10.1038/s42003-021-02480-9
Gauthier J, Boulain H, van Vugt JJFA, Baudry L, Persyn E, Aury JM, Noel B, Bretaudeau A, Legeai F, Warris S, Chebbi MA, Dubreuil G, Duvic B, Kremer N, Gayral P, Musset K, Josse T, Bigot D, Bressac C, Moreau S, Periquet G, Harry M, Montagné N, Boulogne I, Sabeti-Azad M, Maïbèche M, Chertemps T, Hilliou F, Siaussat D, Amselem J, Luyten I, Capdevielle-Dulac C, Labadie K, Merlin BL, Barbe V, de Boer JG, Marbouty M, Cônsoli FL, Dupas S, Hua-Van A, Le Goff G, Bézier A, Jacquin-Joly E, Whitfield JB, Vet LEM, Smid HM, Kaiser L, Koszul R, Huguet E, Herniou EA, Drezen JM. Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Commun Biol. 2021 Jul 30;4(1):940. doi: 10.1038/s42003-021-02480-9. PMID: 34331006; PMCID: PMC8324771.
Copy Download .nbib Format: NLM
Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization.

Methods in molecular biology (Clifton, N.J.)

Matthey-Doret C, Baudry L, Mortaza S, Moreau P, Koszul R, Cournac A.
PMID: 34415528
Methods Mol Biol. 2022;2301:1-15. doi: 10.1007/978-1-0716-1390-0_1.

Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation...

Cite
Matthey-Doret C, Baudry L, Mortaza S, et al. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. Methods Mol Biol. 2022;2301:1-15doi: 10.1007/978-1-0716-1390-0_1.
Matthey-Doret, C., Baudry, L., Mortaza, S., Moreau, P., Koszul, R., & Cournac, A. (2022). Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. Methods in molecular biology (Clifton, N.J.), 23011-15. https://doi.org/10.1007/978-1-0716-1390-0_1
Matthey-Doret, Cyril, et al. "Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization." Methods in molecular biology (Clifton, N.J.) vol. 2301 (2022): 1-15. doi: https://doi.org/10.1007/978-1-0716-1390-0_1
Matthey-Doret C, Baudry L, Mortaza S, Moreau P, Koszul R, Cournac A. Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. Methods Mol Biol. 2022;2301:1-15. doi: 10.1007/978-1-0716-1390-0_1. PMID: 34415528.
Copy Download .nbib Format: NLM
Generation of gene-level resolution chromosome contact maps in bacteria and archaea.

STAR protocols

Cockram C, Thierry A, Koszul R.
PMID: 34027477
STAR Protoc. 2021 May 05;2(2):100512. doi: 10.1016/j.xpro.2021.100512. eCollection 2021 Jun 18.

Chromosome conformation capture (Hi-C) has become a routine method for probing the 3D organization of genomes. However, when applied to bacteria and archaea, current protocols are expensive and limited in their resolution. By dissecting the different steps of published...

Cite
Cockram C, Thierry A, Koszul R. Generation of gene-level resolution chromosome contact maps in bacteria and archaea. STAR Protoc. 2021;2(2):100512doi: 10.1016/j.xpro.2021.100512.
Cockram, C., Thierry, A., & Koszul, R. (2021). Generation of gene-level resolution chromosome contact maps in bacteria and archaea. STAR protocols, 2(2), 100512. https://doi.org/10.1016/j.xpro.2021.100512
Cockram, Charlotte, et al. "Generation of gene-level resolution chromosome contact maps in bacteria and archaea." STAR protocols vol. 2,2 (2021): 100512. doi: https://doi.org/10.1016/j.xpro.2021.100512
Cockram C, Thierry A, Koszul R. Generation of gene-level resolution chromosome contact maps in bacteria and archaea. STAR Protoc. 2021 May 05;2(2):100512. doi: 10.1016/j.xpro.2021.100512. eCollection 2021 Jun 18. PMID: 34027477; PMCID: PMC8121701.
Copy Download .nbib Format: NLM
Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community.

Microbiology resource announcements

Lamy-Besnier Q, Koszul R, Debarbieux L, Marbouty M.
PMID: 33927045
Microbiol Resour Announc. 2021 Apr 29;10(17). doi: 10.1128/MRA.01396-20.

The Oligo-Mouse-Microbiota (OMM

Cite
Lamy-Besnier Q, Koszul R, Debarbieux L, et al. Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community. Microbiol Resour Announc. 2021;10(17)doi: 10.1128/MRA.01396-20.
Lamy-Besnier, Q., Koszul, R., Debarbieux, L., & Marbouty, M. (2021). Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community. Microbiology resource announcements, 10(17), . https://doi.org/10.1128/MRA.01396-20
Lamy-Besnier, Quentin, et al. "Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community." Microbiology resource announcements vol. 10,17 (2021). doi: https://doi.org/10.1128/MRA.01396-20
Lamy-Besnier Q, Koszul R, Debarbieux L, Marbouty M. Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community. Microbiol Resour Announc. 2021 Apr 29;10(17). doi: 10.1128/MRA.01396-20. PMID: 33927045; PMCID: PMC8086220.
Copy Download .nbib Format: NLM
Correction to: Proximity ligation scaffolding and comparison of two .

Biotechnology for biofuels

Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F.
PMID: 29942348
Biotechnol Biofuels. 2018 Jun 13;11:163. doi: 10.1186/s13068-018-1161-5. eCollection 2018.

[This corrects the article DOI: 10.1186/s13068-017-0837-6.].

Cite
Jourdier E, Baudry L, Poggi-Parodi D, et al. Correction to: Proximity ligation scaffolding and comparison of two . Biotechnol Biofuels. 2018;11:163doi: 10.1186/s13068-018-1161-5.
Jourdier, E., Baudry, L., Poggi-Parodi, D., Vicq, Y., Koszul, R., Margeot, A., Marbouty, M., & Bidard, F. (2018). Correction to: Proximity ligation scaffolding and comparison of two . Biotechnology for biofuels, 11163. https://doi.org/10.1186/s13068-018-1161-5
Jourdier, Etienne, et al. "Correction to: Proximity ligation scaffolding and comparison of two ." Biotechnology for biofuels vol. 11 (2018): 163. doi: https://doi.org/10.1186/s13068-018-1161-5
Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F. Correction to: Proximity ligation scaffolding and comparison of two . Biotechnol Biofuels. 2018 Jun 13;11:163. doi: 10.1186/s13068-018-1161-5. eCollection 2018. PMID: 29942348; PMCID: PMC5998568.
Copy Download .nbib Format: NLM
Proximity ligation scaffolding and comparison of two .

Biotechnology for biofuels

Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F.
PMID: 28616075
Biotechnol Biofuels. 2017 Jun 12;10:151. doi: 10.1186/s13068-017-0837-6. eCollection 2017.

BACKGROUND: The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, regarding for instance the evolution...

Cite
Jourdier E, Baudry L, Poggi-Parodi D, et al. Proximity ligation scaffolding and comparison of two . Biotechnol Biofuels. 2017;10:151doi: 10.1186/s13068-017-0837-6.
Jourdier, E., Baudry, L., Poggi-Parodi, D., Vicq, Y., Koszul, R., Margeot, A., Marbouty, M., & Bidard, F. (2017). Proximity ligation scaffolding and comparison of two . Biotechnology for biofuels, 10151. https://doi.org/10.1186/s13068-017-0837-6
Jourdier, Etienne, et al. "Proximity ligation scaffolding and comparison of two ." Biotechnology for biofuels vol. 10 (2017): 151. doi: https://doi.org/10.1186/s13068-017-0837-6
Jourdier E, Baudry L, Poggi-Parodi D, Vicq Y, Koszul R, Margeot A, Marbouty M, Bidard F. Proximity ligation scaffolding and comparison of two . Biotechnol Biofuels. 2017 Jun 12;10:151. doi: 10.1186/s13068-017-0837-6. eCollection 2017. PMID: 28616075; PMCID: PMC5469131.
Copy Download .nbib Format: NLM
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut.

eLife

Marbouty M, Thierry A, Millot GA, Koszul R.
PMID: 33634788
Elife. 2021 Feb 26;10. doi: 10.7554/eLife.60608.

Bacteriophages play important roles in regulating the intestinal human microbiota composition, dynamics, and homeostasis, and characterizing their bacterial hosts is needed to understand their impact. We applied a metagenomic Hi-C approach on 10 healthy human gut samples to unveil...

Cite
Marbouty M, Thierry A, Millot GA, et al. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. Elife. 2021;10doi: 10.7554/eLife.60608.
Marbouty, M., Thierry, A., Millot, G. A., & Koszul, R. (2021). MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. eLife, 10. https://doi.org/10.7554/eLife.60608
Marbouty, Martial, et al. "MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut." eLife vol. 10 (2021). doi: https://doi.org/10.7554/eLife.60608
Marbouty M, Thierry A, Millot GA, Koszul R. MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. Elife. 2021 Feb 26;10. doi: 10.7554/eLife.60608. PMID: 33634788; PMCID: PMC7963479.
Copy Download .nbib Format: NLM
The chiasmatype theory. A new interpretation of the maturation divisions. 1909.

Genetics

Janssens FA, Koszul R, Zickler D.
PMID: 22701051
Genetics. 2012 Jun;191(2):319-46. doi: 10.1534/genetics.112.139725.

No abstract available.

Cite
Janssens FA, Koszul R, Zickler D. The chiasmatype theory. A new interpretation of the maturation divisions. 1909. Genetics. 2012;191(2):319-46doi: 10.1534/genetics.112.139725.
Janssens, F. A., Koszul, R., & Zickler, D. (2012). The chiasmatype theory. A new interpretation of the maturation divisions. 1909. Genetics, 191(2), 319-46. https://doi.org/10.1534/genetics.112.139725
Janssens, F A, et al. "The chiasmatype theory. A new interpretation of the maturation divisions. 1909." Genetics vol. 191,2 (2012): 319-46. doi: https://doi.org/10.1534/genetics.112.139725
Janssens FA, Koszul R, Zickler D. The chiasmatype theory. A new interpretation of the maturation divisions. 1909. Genetics. 2012 Jun;191(2):319-46. doi: 10.1534/genetics.112.139725. PMID: 22701051; PMCID: PMC3374304.
Copy Download .nbib Format: NLM
Modeling Biometric Traits, Yield and Nutritional and Antioxidant Properties of Seeds of Three Soybean Cultivars Through the Application of Biostimulant Containing Seaweed and Amino Acids.

Frontiers in plant science

Kocira S, Szparaga A, Kocira A, Czerwińska E, Wójtowicz A, Bronowicka-Mielniczuk U, Koszel M, Findura P.
PMID: 29636764
Front Plant Sci. 2018 Mar 27;9:388. doi: 10.3389/fpls.2018.00388. eCollection 2018.

In recent years, attempts have been made to use preparations that allow obtaining high and good quality yields, while reducing the application of pesticides and mineral fertilizers. These include biostimulants that are safe for the natural environment and contribute...

Cite
Kocira S, Szparaga A, Kocira A, et al. Modeling Biometric Traits, Yield and Nutritional and Antioxidant Properties of Seeds of Three Soybean Cultivars Through the Application of Biostimulant Containing Seaweed and Amino Acids. Front Plant Sci. 2018;9:388doi: 10.3389/fpls.2018.00388.
Kocira, S., Szparaga, A., Kocira, A., Czerwińska, E., Wójtowicz, A., Bronowicka-Mielniczuk, U., Koszel, M., & Findura, P. (2018). Modeling Biometric Traits, Yield and Nutritional and Antioxidant Properties of Seeds of Three Soybean Cultivars Through the Application of Biostimulant Containing Seaweed and Amino Acids. Frontiers in plant science, 9388. https://doi.org/10.3389/fpls.2018.00388
Kocira, Sławomir, et al. "Modeling Biometric Traits, Yield and Nutritional and Antioxidant Properties of Seeds of Three Soybean Cultivars Through the Application of Biostimulant Containing Seaweed and Amino Acids." Frontiers in plant science vol. 9 (2018): 388. doi: https://doi.org/10.3389/fpls.2018.00388
Kocira S, Szparaga A, Kocira A, Czerwińska E, Wójtowicz A, Bronowicka-Mielniczuk U, Koszel M, Findura P. Modeling Biometric Traits, Yield and Nutritional and Antioxidant Properties of Seeds of Three Soybean Cultivars Through the Application of Biostimulant Containing Seaweed and Amino Acids. Front Plant Sci. 2018 Mar 27;9:388. doi: 10.3389/fpls.2018.00388. eCollection 2018. PMID: 29636764; PMCID: PMC5880921.
Copy Download .nbib Format: NLM
Metagenomes Binning Using Proximity-Ligation Data.

Methods in molecular biology (Clifton, N.J.)

Marbouty M, Koszul R.
PMID: 34415535
Methods Mol Biol. 2022;2301:163-181. doi: 10.1007/978-1-0716-1390-0_8.

Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently,...

Cite
Marbouty M, Koszul R. Metagenomes Binning Using Proximity-Ligation Data. Methods Mol Biol. 2022;2301:163-181doi: 10.1007/978-1-0716-1390-0_8.
Marbouty, M., & Koszul, R. (2022). Metagenomes Binning Using Proximity-Ligation Data. Methods in molecular biology (Clifton, N.J.), 2301163-181. https://doi.org/10.1007/978-1-0716-1390-0_8
Marbouty, Martial, and Koszul, Romain. "Metagenomes Binning Using Proximity-Ligation Data." Methods in molecular biology (Clifton, N.J.) vol. 2301 (2022): 163-181. doi: https://doi.org/10.1007/978-1-0716-1390-0_8
Marbouty M, Koszul R. Metagenomes Binning Using Proximity-Ligation Data. Methods Mol Biol. 2022;2301:163-181. doi: 10.1007/978-1-0716-1390-0_8. PMID: 34415535.
Copy Download .nbib Format: NLM
Cohesin regulates homology search during recombinational DNA repair.

Nature cell biology

Piazza A, Bordelet H, Dumont A, Thierry A, Savocco J, Girard F, Koszul R.
PMID: 34750581
Nat Cell Biol. 2021 Nov;23(11):1176-1186. doi: 10.1038/s41556-021-00783-x. Epub 2021 Nov 08.

Homologous recombination repairs DNA double-strand breaks (DSB) using an intact dsDNA molecule as a template. It entails a homology search step, carried out along a conserved RecA/Rad51-ssDNA filament assembled on each DSB end. Whether, how and to what extent...

Cite
Piazza A, Bordelet H, Dumont A, et al. Cohesin regulates homology search during recombinational DNA repair. Nat Cell Biol. 2021;23(11):1176-1186doi: 10.1038/s41556-021-00783-x.
Piazza, A., Bordelet, H., Dumont, A., Thierry, A., Savocco, J., Girard, F., & Koszul, R. (2021). Cohesin regulates homology search during recombinational DNA repair. Nature cell biology, 23(11), 1176-1186. https://doi.org/10.1038/s41556-021-00783-x
Piazza, Aurèle, et al. "Cohesin regulates homology search during recombinational DNA repair." Nature cell biology vol. 23,11 (2021): 1176-1186. doi: https://doi.org/10.1038/s41556-021-00783-x
Piazza A, Bordelet H, Dumont A, Thierry A, Savocco J, Girard F, Koszul R. Cohesin regulates homology search during recombinational DNA repair. Nat Cell Biol. 2021 Nov;23(11):1176-1186. doi: 10.1038/s41556-021-00783-x. Epub 2021 Nov 08. PMID: 34750581.
Copy Download .nbib Format: NLM
Showing 1 to 12 of 16 entries