A rationalized definition of general tumor suppressor microRNAs excludes miR-34a
Sophie Mockly, Élisabeth Houbron, Hervé Seitz
Systemic impact of small regulatory RNAs
Genetics, cell biology and development
MicroRNAs ("miRNAs") are small post-transcriptional regulators. The function of these small RNAs in animals has been well characterized at a molecular level, but their role is less well known at the macroscopic scale: how could miRNAs have any biological function if they repress most of their targets less than 2-fold (while inter-individual gene expression fluctuation typically exceeds 2-fold, and is buffered by homeostatic mechanisms)?
According to the current dogma, each miRNA regulates tens or hundreds of targets, yet several observations suggest miRNAs have a much weaker impact on animal biology. Our recent work also suggests that both experimental and computational miRNA target identification methods are heavily contaminated with false positives: these false positives may be truly repressed by miRNAs at the molecular scale, but such a small repressive effect fails to translate into a macroscopic phenotype for most genes.
Our work thus suggests that the biological role of miRNAs has been largely over-estimated. We are currently exploring practical consequences of this new theoretical framework, measuring the contribution of individual miRNA/target interactions to global in vivo phenotypes.
More generally, we are proposing a new vision of gene regulation: a regulatory target is not simply a gene that is affected by a regulatory pathway; it is a gene that is affected enough by the pathway – the extent of a measured regulation needs to be confronted to the robustness of biological systems to fluctuations.
To contact us by email: each of our email addresses follows the format first_name.family_name[at]igh.cnrs.fr (without accents)
Publications of the team
Re-assessment of the involvement of Snord115 in the serotonin 2C receptor pathway in a genetically relevant mouse model.
Hebras J, Marty V, Personnaz J, Mercier P, Krogh N, Nielsen H, Aguirrebengoa M, Seitz H, Pradere JP, Guiard BP, Cavaille J
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation
Patricia Richard, Shuang Feng, Yueh-Lin Tsai, Wencheng Li, Paola Rinchetti, Ubayed Muhith, Juan Irizarry-Cole, Katharine Stolz, Lionel A Sanz, Stella Hartono, Mainul Hoque, Saba Tadesse, Hervé Seitz, Francesco Lotti, Michio Hirano, Frédéric Chédin, Bin Tian, James L Manley
Prospects and challenges of multi-omics data integration in toxicology.
Canzler S, Schor J, Busch W, Schubert K, Rolle-Kampczyk UE, Seitz H, Kamp H, von Bergen M, Buesen R, Hackermüller J
+
Systemic impact of small regulatory RNAs
Prospects and challenges of multi-omics data integration in toxicology.
Canzler S, Schor J, Busch W, Schubert K, Rolle-Kampczyk UE, Seitz H, Kamp H, von Bergen M, Buesen R, Hackermüller J
+
Systemic impact of small regulatory RNAs
Inconsistencies and Limitations of Current MicroRNA Target Identification Methods.
Mockly S, Seitz H
Editorial: miRNA Regulatory Pathways in Metazoans. Advances From in vivo and ex vivo Studies.
Amar L, Seitz H
On the number of functional microRNA targets.
Seitz H
Functional lability of RNA-dependent RNA polymerases in animals.
Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H
Amphioxus functional genomics and the origins of vertebrate gene regulation.
Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M
Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop.
Buesen R, Chorley BN, da Silva Lima B, Daston G, Deferme L, Ebbels T, Gant TW, Goetz A, Greally J, Gribaldo L, Hackermüller J, Hubesch B, Jennen D, Johnson K, Kanno J, Kauffmann HM, Laffont M, McMullen P, Meehan R, Pemberton M, Perdichizzi S, Piersma AH, Sauer UG, Schmidt K, Seitz H, Sumida K, Tollefsen KE, Tong W, Tralau T, van Ravenzwaay B, Weber RJM, Worth A, Yauk C, Poole A
microRNA target prediction programs predict many false positives
Pinzon, N., Li, B., Martinez, L., Sergeeva, A., Presumey, J., Apparailly, F., Seitz, H
Issues in current microRNA target identification methods
Seitz H
The gastrula transition reorganizes replication origin selection in Caenorhabditis elegans
Rodríguez-Martínez, M., Pinzón, N., Ghommidh, C., Beyne, E., Seitz, H., Cayrou, C., Méchali, M.
+
Replication and Genome Dynamics
Advancing the use of noncoding RNA in regulatory toxicology: Report of an ECETOC workshop
Aigner A, Buesen R, Gant T, Gooderham N, Greim H, Hackermüller J, Hubesch B, Laffont M, Marczylo E, Meister G, Petrick JS, Rasoulpour RJ, Sauer UG, Schmidt K, Seitz H, Slack F, Sukata T, van der Vies SM, Verhaert J, Witwer KW, Poole A
Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner
Eckenfelder A, Ségéral E, Pinzón N, Ulveling D, Amadori C, Charpentier M, Nidelet S, Concordet JP, Zagury JF, Paillart JC, Berlioz-Torrent C, Seitz H, Emiliani S, Gallois-Montbrun S.
Coding and non-coding variants in the SHOX2 gene in patients with early-onset atrial fibrillation
Hoffmann S, Clauss S, Berger IM, Weiß B, Montalbano A, Röth R, Bucher M, Klier I, Wakili R, Seitz H, Schulze-Bahr E, Katus HA, Flachsbart F, Nebel A, Guenther SP, Bagaev E, Rottbauer W, Kääb S, Just S, Rappold GA.
microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus
Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM
Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation
Royo H, Seitz H, ElInati E, Peters AH, Stadler MB, Turner JM
Cnidarian microRNAs frequently regulate targets by cleavage
Moran, Y., Fredman, D., Praher, D., Li Z. L., Meng Wee,L., Rentzsch, F., Zamore,P.D., Technau, U., Seitz H.
Insect small non-coding RNA involved in epigenetic regulations
Chambeyron, S., Seitz, H.
+
Non-coding RNA, epigenetics and genome stability
Quantitative aspects of RNA silencing in metazoans
Sergeeva, A., Restrepo, N.P., and Seitz, H.
Recognition of the pre-miRNA structure by Drosophila Dicer-1
Tsutsumi A, Kawamata T, Izumi N, Seitz H, Tomari Y
A 5´-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation
Seitz H, Tushir JS, Zamore PD
#}
Thèses
Topic : Reciprocal repressions between microRNA and messenger RNA
Sophie MOCKLY 01/10/2017 - 31/12/2021
Thesis supervisor : Hervé SEITZ
Publications during the thesis :
1. Mockly S. et Seitz H. Inconsistencies and limitations of current microRNA target identification methods (2019) Methods Mol Biol, 1970:291-314 (lien Pubmed : https://pubmed.ncbi.nlm.nih.gov/30963499/)
2. Mockly S., Houbron É et Seitz H. A rationalized definition of tumor suppressor microRNAs excludes miR-34a (soumis, manuscrit accessible à : https://www.biorxiv.org/content/10.1101/2021.02.11.430795v4)
InteRNAt summer school
2021 issue of the InteRNAt summer school (November 2–6, 2021, in Sète):
Website of the event : https://internat21.sciencesconf.org/.
2019 issue of the InteRNAt summer school (October 6–10, 2019, in Sète):
Website of the event : https://internat.sciencesconf.org.
Content of the introductory lectures given during the first half-day of the summer school (in French)(introduction on RNAi, on microRNAs, and on the biochemistry of the RISC complex; exercises): freely downloadable here.
Collaborators
| Collaborator | Aim of the collaboration | Common publications |
|---|---|---|
| Dr. Yukihide TOMARI (université de Tõkyõ) Web site |
Analysis of structural determinants of microRNA biogenesis | Kawamata et al. (2009) Pubmed Tsutsumi et al. (2011) Pubmed |
| Dr. Ulrich TECHNAU (université de Vienne) Web site |
Functional analysis of small regulatory RNAs in Nematostella vectensis | Moran et al. (2014) Pubmed |
| Dr. Fabian RENTZSCH (SARS Center) Web site |
Functional analysis of small regulatory RNAs in Nematostella vectensis | Moran et al. (2014) Pubmed |
| Prof. Phillip D. ZAMORE (école de médecine de l'université du Massachusetts) Web site |
Functional analysis of small regulatory RNAs in Nematostella vectensis | Moran et al. (2014) Pubmed |
| Dr. James TURNER (Crick Institute, Londres) Web site |
Analysis of the expression of microRNAs subjected to an epigenetic control in mammals | Royo et al. (2015) Pubmed |
| Dr. Denis TAGU (INRA Rennes) Web site |
Characterization of small regulatory RNAs in pea aphid | |
| Dr. Florence APPARAILLY (IRMB, Montpellier) Web site |
Measurement of inter-individual fluctuation in gene expression in neutrophils | Pinzón et al. (2017) Pubmed |
| Dr. Marcel MÉCHALI (IGH, Montpellier) Web site |
Identification of replication origins in early Nematode development and epigenetic characterization | Rodríguez-Martínez et al. (2017) Pubmed |
| Dr. Mark COCK (UMR 8227, Roscoff) Web site |
MicroRNA identification in the brown alga Ectocarpus silicosus | Tarver et al. (2015) Pubmed |
| Prof. Gudrun RAPPOLD (UniversitätKlinikum, Heidelberg) Web site |
Identification of a microRNA binding site specific to patients with atrial fibrillation | Hoffmann et al. (2016) Pubmed |
| Dr. Hector ESCRIVA (Observatoire océanologique de Banyuls) Web site |
Characterization of small RNAs in the cephalochordate Branchiostoma lanceolatum |
Marlétaz et al. (2018) Pubmed Pinzón et al. (2019) Pubmed |
| Dr. Sarah GALLOIS-MONTBRUN (Institut Cochin, Paris) Web site |
Identification of Ago binding sites in HIV-1 viral RNA | Eckenfelder et al. (2017) Pubmed |
| Dr. James Manley (Columbia university, New York, États-Unis) Web site |
Characterization of molecular consequences of SETX repression in human cells | Richard et al. (2020) Pubmed |
| Dr. Jérôme Cavaillé (CBI, Toulouse) Web site |
Evaluation of molecular and physiological consequences of the deletion of the SNORD115 RNA |
Hebras et al. (2020) Pubmed |
Slides of seminars given in public lecture
- December 8, 2022 for the Cambridge RNA Club : 25 minutes slideshow (speaker: Hervé Seitz)
- November 28, 2022 for the association « Lattes université pour tous » : 2h slideshow (speaker: Hervé Seitz)
- November 10, 2022 for the colloquium "Bioinformatics in toxicology" at the INRS Nancy: 1h slideshow (speaker: Hervé Seitz)
- October 28, 2022 for the colloquium "Scientific Research: Emerging Concepts and Ethical Challenges" of Lebanon's Conseil National de la Recherche Scientifique and IGH : 45 minutes slideshow (speaker : Hervé Seitz)
- October 12, 2022 for the association "Luz'Arts" in St-Georges-de-Luzençon 30 minute slideshow (speaker: Hervé Seitz)
- April 13, 2022, for the association « Rando Loisirs Culture » (Grabels, France) : 2h slideshow (speaker : Hervé Seitz)
- March 16, 2022, for the association « Lattes université pour tous » : 1h slideshow (speaker : Hervé Seitz)
- January 25, 2022 for the Montpellier university doctoral college : 30 minutes slideshow (speaker: Hervé Seitz)
- November 8, 2021 or the Small RNA Bioinformatics club : 30 minutes slideshow (speaker: Hervé Seitz); video record of the conference: link.
- November 8, 2021 or the Small RNA Bioinformatics club : 8 minutes slideshow (speaker : Sophie Mockly) ; video record of the conference : link.
- October 5, 2021 for Master 2 students in ecology at the university of Montpellier: 3h slideshow (speaker: Hervé Seitz)
- April 21, 2021 for the Cancéropôle Grand Sud-Ouest (Axis 2): 25 minutes slideshow (speaker: Hervé Seitz)
- March 13, 2021 for the association "Cercle zététique du Languedoc-Roussillon" (Montpellier, France): 2h slideshow (speaker: Hervé Seitz)
Video record of the conference (in French): conference; questions/answers with the audience. - February 2, 2021 at the CRCT Cancer research center of Toulouse: 50 minute slideshow (speaker: Hervé Seitz)
- September 28, 2020, for Master 2 students in ecology at the university of Montpellier: 4h30 slideshow (speaker: Hervé Seitz)
- November 28, 2019 at the colloquium Santé et droit de choisir (Clermont-Ferrand, France): 30 minute slideshow (in French) (speaker: Hervé Seitz).
- October 17, 2019 for the Visiatome (Marcoule, France): 1h slideshow (speaker: H. Seitz)
- May 15, 2019 for the association "Rando, Loisirs, Culture" (Grabels, France): 2h slideshow (speaker: Hervé Seitz)
- April 10, 2019 for the M1 masters students of Montpellier university : 15 minute slideshow (speaker: Hervé Seitz)
- January 23, 2019 at the Université du Tiers Temps (Montpellier, France): 50 minute slideshow (speaker: Hervé Seitz)
- January 16, 2019 at the Université du Tiers Temps (Montpellier, France): 50 minute slideshow (speaker: Hervé Seitz)
- November 23, 2018 at the Young Life Scientist meeting (Montpellier, France): 15 minute slideshow (speaker: Hervé Seitz)
- November 21, 2018 at the Journées Cancéropôle Grand Sud-Ouest (la Grande-Motte, France): 15 minute slideshow (speaker: H. Seitz)
- November 7, 2018 at the 11th SifrARN meeting (Nancy, France): 25 minute slideshow (speaker: H. Seitz)
- October 19, 2018 at the colloquium on Artificial intelligence in biology and health (Montpellier, France) : 30 minute slideshow (speaker: H. Seitz)
- April 25, 2018 at the "Café des sciences" (Avignon, France): 15 minute slideshow (in French) (speaker: H. Seitz)
- March 13, 2018 at the colloquium Quelles limites pour les technosciences en santé ? (Clermont-Ferrand, France): 30 minute slideshow (in French) (speaker: H. Seitz).
- February 8, 2018 at the International course on Non-coding genome of Curie institute (Paris, France): 1h slideshow (speaker: H. Seitz).
- May 16, 2017 at the Colloque inter-LabEx CRISPR-Cas9 (Montpellier, France) : 15 minute slideshow (speaker: H. Seitz).
- June 27, 2016 at the Tõkyõ ncRNA symposium "Clues to non-coding RNA taxonomy" (Tõkyõ, Japon) : 15 minute slideshow (speaker: H. Seitz).
- March 3, 2016 at the ECETOC Workshop "ncRNAs and Risk Assessment Science" (Málaga, Spain): 15 minute slideshow (speaker: H. Seitz).
- February 20, 2017 at the Université du Tiers Temps (Montpellier, France): 1h slideshow (speaker : Isabelle Busseau)
- February 12, 2016 at the SMPGD (Statistical methods for post genomic data) annual workshop (Lille, France): 45 minute slideshow (speaker : H. Seitz).
- January 25, 2016 at the Keystone Symposium "Small RNA Silencing: Little Guides, Big Biology (A6)" (Keystone, U.S.): 12 minute slideshow (speaker : N. Pinzón).
- January 15, 2016 for the Centre d'éthique contemporaine de Montpellier : 1h slideshow (speaker : Isabelle Busseau)
- June 4, 2015 at the ESPE Science School "Non-coding RNAs in paediatric endocrinology" (Annecy, France): 30 minute slideshow (speaker : H. Seitz).
- June 9, 2014 at the Taiwan-France mini-symposium on regulatory RNAs (Taipei, Taïwan) : 40 minute slideshow (speaker: H. Seitz).
- February 27, 2014 for the L2 students in philosophy at the university Montpellier III: 1h slideshow (speaker: Isabelle Busseau)
- February 2, 2014 at the Keystone Symposium "RNA silencing (A9)" (Seattle, U.S.): 12 minute slideshow (speaker : H. Seitz).
- November 26, 2013 at the symposium Statistical analysis of RNA-seq data: advances and challenges of Pasteur institute (Paris, France): 45 minute slideshow (speaker : H. Seitz).
- March 22, 2013 at the Keystone Symposium "RNA silencing (C7)" (Whistler, Canada): 12 minute slideshow (speaker: H. Seitz).
- December 11, 2012 at the International course on Non-coding genome of Curie institute (Paris, France): 1h slideshow (speaker : H. Seitz).
- October 13, 2012 at the BTCure miRNA workshop (Montpellier, France): 30 minute slideshow (speaker : H. Seitz).
- September 12, 2012 at the Annual French conference on Drosophila (Clermont-Ferrand, France): 30 minute slideshow (speaker : H. Seitz).
- August 30, 2012 at the Cold Spring Harbor Laboratory Meeting "Regulatory and Non-coding RNAs" (Cold Spring Harbor, U.S.): 15 minute slideshow (speaker : N. Pinzón).
- April 24, 2012 at the Schlumberger Foundation conference "Small Silencing RNA Biology and Mechanism" (Tourtour, France): 1h slideshow (speaker: H. Seitz).
- June 15, 2011 at the Sixteenth annual meeting of the RNA society (Kyōto, Japan): 12 minute slideshow (speaker: H. Seitz).
- June 13, 2011 at the Tōkyō RNA club symposium (Tōkyō, Japan): 15 minute slideshow (speaker: H. Seitz).
- June 10, 2011 at the Fifth annual Arthropod genomics symposium (Kansas City, U.S.): 30 minute slideshow (speaker: H. Seitz).
- December 2, 2010 at the Fifth European workshop on immune-mediated inflammatory diseases (Sitges, Spain): 30 minute slideshow (speaker: H. Seitz).
- May 19, 2009 at the Microsymposium on small RNAs (Vienna, Austria): 30 minute slideshow (speaker: H. Seitz).
Computer programs
Manuscrit "Mockly et al., 2022"
Manuscrit “Pinzón et al., 2019”
- Téléchargement des protéomes prédits de Métazoaires - 3.6Go
- Recherche de candidats RdRP et re-séquençage du locus “BL09945” - 21.6Mo
- Phylogénie de la famille des “RdRP eucaryotiques” 71.8Mo
- Analyse du Small RNA-Seq de Branchiostoma lanceolatum 4.4Go
- Petits ARN issus des pathogènes avérés ou potentiels 20.2Mo
| Nom de fichier | Taille |
|---|---|
| 00_Proteome_download.md | 12.65 KB |
| All_predicted_proteomes.tar.bz2 | 3.31 GB |
| ailable_at_Ensembl.txt" target="_blank">Available_at_Ensembl.txt | 3.09 KB |
| Module_measures_proteome_size_dist.pl | 485 bytes |
| Protein_lengths_in_predicted_proteomes.tar.bz2 | 19.55 MB |
| R_commands_statistics_on_protein_lengths | 1.1 KB |
| Species_with_at_least_1000_proteins_of_more_than_1000aa.txt | 8.35 KB |
| Species_with_at_least_5000_proteins_of_more_than_500aa.txt | 7.21 KB |
| genomes_overview.txt | 53.05 KB |
| Nom de fichier | Taille |
|---|---|
| 01_RdRP_search.md | 10.65 KB |
| Clone4.fa | 2.87 KB |
| Clone5.fa | 2.89 KB |
| Every_PFAM_RdRP_evening_hitdata_concise.txt.bz2 | 178.25 KB |
| Every_PFAM_RdRP_evening_hitdata_full.txt.bz2 | 1.7 MB |
| Every_PFAM_RdRP_evening_hitdata_standard.txt.bz2 | 459.97 KB |
| Fuses_lines_clean.pl | 514 bytes |
| Order_11104254864-1_Results.zip | 9.08 MB |
| Order_11104283914-1_Results.zip | 7.77 MB |
| R_commands_piecharts | 352 bytes |
| RdRP_profiles.tar.bz2 | 650.82 KB |
| Sequences_candidates_every_PFAM_RdRP.fa.bz2 | 816.88 KB |
| Nom de fichier | Taille |
|---|---|
| 02_RdRP_phylogeny.md | 1.49 KB |
| Cipres_DataMARSV1short3MBLG.zip | 77.66 MB |
| RDRPMARSV1alignHMMALIGNShortV3TRIM.fasta | 206.61 KB |
| RdRPMARSV1.fa | 467.16 KB |
| STDERR | 0 bytes |
| STDOUT | 1.25 MB |
| _JOBINFO.TXT | 347 bytes |
| _scheduler_stderr.txt | 634 bytes |
| done.txt | 49 bytes |
| infile.nex.bz2 | 80.16 KB |
| infile.nex.ckp.bz2 | 83.41 KB |
| infile.nex.ckp7E.bz2 | 83.35 KB |
| infile.nex.con.tre.bz2 | 36.9 KB |
| infile.nex.mcmc.bz2 | 10.85 KB |
| infile.nex.parts.bz2 | 11.96 KB |
| infile.nex.run1.p.bz2 | 113.92 KB |
| infile.nex.run1.t.bz2 | 33.64 MB |
| infile.nex.run2.p.bz2 | 113.8 KB |
| infile.nex.run2.t.bz2 | 33.34 MB |
| infile.nex.trprobs.bz2 | 625.68 KB |
| infile.nex.tstat.bz2 | 8 KB |
| infile.nex.vstat.bz2 | 30.3 KB |
| ns/page_white_text.png" />paramfile.txt | 61 bytes |
| scheduler.conf | 65 bytes |
| ns/page_white_text.png" />start.txt | 40 bytes |
| ns/page_white_text.png" />stderr.txt | 0 bytes |
| ns/page_white_text.png" />stdout.txt | 1.25 MB |
| ns/page_white_text.png" />term.txt | 318 bytes |
| Nom de fichier | Taille |
|---|---|
| 04_Pathogen_and_potential_pathogen_matching_reads.md | 24.99 KB |
| ATCV1_contig_mappers.tar.bz2 | 1.91 KB |
| ATCV1_genome.fa | 285.38 KB |
| All_medium_and_long_contigs.xml.bz2 | 13.94 MB |
| Chef.sh | 1.36 KB |
| Chef2.sh | 971 bytes |
| Chef_ATCV1.sh | 1.3 KB |
| ns/page_white_text.png" />Contig_name_correspondance.txt | 3.99 MB |
| Module_parse_XML.pl | 1.67 KB |
| R_commands_ATCV1_size_dist | 750 bytes |
| R_commands_contig_length_statistics | 99 bytes |
| R_commands_legended_mapping_on_contig | 1.74 KB |
| R_commands_mapping_on_bacterial_genomes | 1.73 KB |
| R_commands_mapping_on_contig | 1.74 KB |
| R_commands_mapping_on_viral_contig | 1.28 KB |
| R_commands_mapping_on_viral_contig_all_stages_together | 1.5 KB |
| R_commands_mapping_on_viral_genome | 1.74 KB |
| R_commands_pathogenic_bacteria_size_dist | 810 bytes |
| R_commands_top_contig_size_dist | 815 bytes |
| Staphylococcus_aureus_genome.fa.bz2 | 783.99 KB |
| Unified_contigs.fa | 3.06 MB |
| Vibrio_alginolyticus_genome.fa.bz2 | 1.41 MB |
| Vibrio_anguillarum_genome.fa.bz2 | 1.12 MB |
| Viral_contigs.fa | 600 bytes |
Manuscrit "Mockly et Seitz, 2019"
- Scripts et données pour la préparation de la Table 1 :
Mockly_and_Seitz_Table1.tar.bz2
Manuscrit "Pinzón et al., 2017"
- Comparaison de l'amplitude de la répression guidée par miR-223 à la variabilité inter-individu dans l'expression des cibles : code source et fichiers de données.
- Quantification absolue des ARNm des cellules C2C12 au cours de la différenciation : code source et fichiers de données.
- Comparaison globale de la sensibilité des gènes au dosage et de la conservation des sites d'interaction aux miARN : code source et fichiers de données.
Scripts et données pour la préparation des 6 figures :
- Figure_1.tar.bz2
- Figure_2.tar.bz2
- Figure_3.tar.bz2
- Figure_4.tar.bz2
- Figure_5.tar.bz2
- Figure_6.tar.bz2
Conversion des fichiers FCS de cytométrie en fichiers texte
- Script de conversion (usage : ./read_FCS.py input.fcs output.txt) : script python.
Tutorials
1. Unix training
- First lecture: browsing the arborescence, manipulating files, tricks and advice, redirecting to a file, grep, combining commands
- Second lecture: the nano text editor, writing and executing scripts, sedSecond lecture: the nano text editor, writing and executing scripts, sed
2. Statistics in molecular biology
- Introductory statistics for biologists
- Slideshow (in French) of the 7h lecture given for technical training for CNRS staff (initially given on November 7, 2022)
3. R training
- First lecture: basic commands
- Second lecture: tracing graphs
- Third lecture: a few statistical tests
- Fourth lecture: a few advanced commands
- Slideshow (in French) of the 14h lecture given for technical training for CNRS staff (initially given on November 8 and 9, 2022)
- Slideshow (in French) of the 3h30 lecture given for technical training for CNRS staff (initially given on November 16, 2022) and data files necessary for the exercises
4. Videos of master classes
Activity reports and evaluation
Context :
CNRS researchers have to submit every year a yearly activity report, and every 5 years they have to submit a “phased activity report” which is more detailed (as well as a “mid-phase activity report” in the middle of that 5 year-period). Following the merge of regions Midi-Pyrénées and Languedoc-Roussillon, laboratories in Languedoc-Roussillon joined the phase of Midi-Pyrénées laboratories, thus delaying by one year the evaluation which was scheduled for 2019 (it will take place in 2020).
In addition, laboratories are evaluated every 5 to 6 years by an international committee, which is assembled by HCERES (formerly known as AERES), which will then issue an evaluation report (in English).
Activity reports and evaluation reports for our team:
2022 mid-phase activity report of Hervé Seitz (December 2019 – June 2022) (in French)
2020 evaluation report of our team by HCERES (in English)
2020 phased activitiy report of Hervé Seitz (January 2014 – December 2019) (in French)
2016 mid-phase activity report of Hervé Seitz (January 2014 – September 2016) (in French)
2014 evaluation report of our team by AERES (in English)
2014 phased activity report of Hervé Seitz (January 2009 – December 2013) (in French)
Pour le grand public
« La technologie CRISPR/Cas9 »
(compte-rendu de la conférence donnée par Hervé Seitz au colloque « Quelles limites pour les technosciences en santé ? » à Clermont-Ferrand le 13 mars 2018, et publié dans le n°15 de la Revue du Centre Michel de l'Hospital).
Parallèle entre l'informatique et la génétique
(édition du génome, débuggage, matérialité de l'information, ...) (interview donnée dans le cadre des Tic-Talks du LIG).
Les statistiques en science expérimentale. Principe, limitations, erreurs courantes, illustrées par les rumeurs pseudo-scientifiques sur la Covid-19
(visio-conférence donnée le 13 mars 2021 sur invitation du cercle zététique du Languedoc-Roussillon ; diaporama cliquable accessible ici).
