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Bibliography

References to publications, sorted by year and author.

Berio, F, Bayle, Y, Baum, D, Goudemand, N, and Debiais-Thibaud, M (2022).
Hide and seek shark teeth in Random Forests: Machine learning applied to Scyliorhinus canicula
PeerJ, 10:e13575.

Boumpas, P, Merabet, S, and Carnesecchi, J (2022).
Integrating transcription and splicing into cell fate: Transcription factors on the block
Wiley Interdiscip Rev RNA:e1752.

Cerutti, C, Zhang, L, Tribollet, V, Shi, JR, Brillet, R, Gillet, B, Hughes, S, Forcet, C, Shi, TL, and Vanacker, JM (2022).
Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets
Sci Rep, 12(1):3826.

Delage, L, Lambert, M, Bardel, E, Kundlacz, C, Chartoire, D, Conchon, A, Peugnet, AL, Gorka, L, Auberger, P, Jacquel, A, Soussain, C, Destaing, O, Delecluse, HJ, Delecluse, S, Merabet, S, Traverse-Glehen, A, Salles, GA, Bachy, E, Billaud, M, Ghesquieres, H, Genestier, L, Rouault, JP, and Sujobert, P (2022).
BTG1 inactivation drives lymphomagenesis and promotes lymphoma dissemination through activation of BCAR1
Blood.

Etchegaray, E, Baas, D, Naville, M, Haftek-Terreau, Z, and Volff, JN (2022).
The neurodevelopmental gene MSANTD2 belongs to a gene family formed by recurrent molecular domestication of Harbinger transposons at the base of vertebrates
Mol Biol Evol.

Finet, C, Decaras, A, Rutkowska, M, Roux, P, Collaudin, S, Joncour, P, Viala, S, and Khila, A (2022).
Leg length and bristle density, both necessary for water surface locomotion, are genetically correlated in water striders
Proc Natl Acad Sci U S A, 119(9).

Flamant, F, Zekri, Y, and Guyot, R (2022).
Functional definition of thyroid hormone response elements based on a synthetic STARR-seq screen
Endocrinology.

Guan, W, Bellemin, S, Bouchet, M, Venkatasubramanian, L, Guillermin, C, Laurençon, A, Kabir, C, Darnas, A, Godin, C, Urdy, S, Mann, R, and Enriquez, J (2022).
Post-transcriptional regulation of transcription factor codes in immature neurones drives neuronal diversity
Cell Reports, 39:110992.

Idoux, R, Bretaud, S, Berthier, C, Ruggiero, F, Jacquemond, V, and Allard, B (2022).
Superfast excitation-contraction coupling in adult zebrafish skeletal muscle fibers
J Gen Physiol, 154(9).

Malbouyres, M, Guiraud, A, Lefrançois, C, Salamito, M, Nauroy, P, Bernard, L, Sohm, F, Allard, B, and Ruggiero, F (2022).
The myotendinous junction marker collagen XXII enables zebrafish postural control learning and optimal swimming performance through its force transmission activity
Matrix Biol, 109:1-18.

Nikolopoulos, N, Matos, RC, Courtin, P, Ayala, I, Akherraz, H, Simorre, JP, Chapot-Chartier, MP, Leulier, F, Ravaud, S, and Grangeasse, C (2022).
DltC acts as an interaction hub for AcpS, DltA and DltB in the teichoic acid D-alanylation pathway of Lactiplantibacillus plantarum
Sci Rep, 12(1):13133.

Paris, M, Wolff, C, Patel, NH, and Averof, M (2022).
The crustacean model Parhyale hawaiensis
Curr Top Dev Biol, 147:199–230.

Shin, J, Paek, KY, Chikhaoui, L, Jung, S, Ponny, S, Suzuki, Y, Padmanabhan, K, and Richter, JD (2022).
Oppositional poly(A) tail length regulation by FMRP and CPEB1
RNA, 28(5):756–765.

Sinigaglia, C, Almazán, A, Lebel, M, Sémon, M, Gillet, B, Hughes, S, Edsinger, E, Averof, M, and Paris, M (2022).
Distinct gene expression dynamics in developing and regenerating crustacean limbs
Proc Natl Acad Sci U S A, 119(27):e2119297119.

Souquet, L, Guenser, P, Girard, C, Mazza, M, Rigo, M, and Goudemand, N (2022).
Temperature-driven heterochrony as a main evolutionary response to climate changes in conodonts
Proc Biol Sci, 289(1985):20220614.

Sugawara, K, Çevrim, C, and Averof, M (2022).
Tracking cell lineages in 3D by incremental deep learning
Elife, 11:e69380.

Tartour, K and Padmanabhan, K (2022).
The Clock Takes Shape—24 h Dynamics in Genome Topology
Frontiers in Cell and Developmental Biology, 9(Article 799971).

Tartour, K, Andriani, F, Folco, EG, Letkova, D, Schneider, R, Saidi, I, Sato, T, Welz, PS, Benitah, SA, Allier, C, and Padmanabhan, K (2022).
Mammalian PERIOD2 regulates H2A.Z incorporation in chromatin to orchestrate circadian negative feedback
Nat Struct Mol Biol.

Tribollet, V, Cerutti, C, Géloën, A, Berger, E, De Mets, R, Balland, M, Courchet, J, Vanacker, JM, and Forcet, C (2022).
ERRα coordinates actin and focal adhesion dynamics
Cancer Gene Ther.

Zekri, Y, Guyot, R, and Flamant, F (2022).
An Atlas of Thyroid Hormone Receptors' Target Genes in Mouse Tissues
Int J Mol Sci, 23(19).

Zekri, Y, Guyot, R, Suñer, IG, Canaple, L, Stein, AG, Petit, JV, Aubert, D, Richard, S, Flamant, F, and Gauthier, K (2022).
Brown adipocytes local response to thyroid hormone is required for adaptive thermogenesis in adult male mice
Elife, 11.

Salamito, M, Nauroy, P, and Ruggiero, F (2021 ).
The Collagen Superfamily: Everything You Always Wanted to Know. F. Ruggiero (Ed). The collagen superfamily and collagenopathies
Biology of Extracellular Matrix, Book chapter, Springer, 8.

Barbier, J, Vaillant, C, Volff, JN, Brunet, FG, and Audit, B (2021).
Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution
Genes (Basel), 12(6).

Carnesecchi, J, Boumpas, P, van Nierop Y Sanchez, P, Domsch, K, Pinto, HD, Borges Pinto, P, and Lohmann, I (2021).
The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II
Nucleic Acids Res.

Darnaud, M, De Vadder, F, Bogeat, P, Boucinha, L, Bulteau, AL, Bunescu, A, Couturier, C, Delgado, A, Dugua, H, Elie, C, Mathieu, A, Novotná, T, Ouattara, DA, Planel, S, Saliou, A, Šrůtková, D, Yansouni, J, Stecher, B, Schwarzer, M, Leulier, F, and Tamellini, A (2021).
A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes
Nat Commun, 12(1):6686.