Difference between revisions of "Publications"

From PastDB

 
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
  
−
==== Main VastDB publication (v1.0) ====
+
==== PastDB publication ====
 +
* Martin, G., Marquez, Y., Duque, P., Irimia, M. (2020). Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions reveal major differences with animals. In preparation.
 +
 
 +
====  VastDB publication (v1.0) ====
 
* Tapial, J., Ha, K. C. H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B. J., Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. ''Genome Research, 27''(10), 1759–1768. [[http://genome.cshlp.org/content/27/10/1759.long link]] [[https://www.ncbi.nlm.nih.gov/pubmed/28855263 PubMed]]
 
* Tapial, J., Ha, K. C. H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B. J., Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. ''Genome Research, 27''(10), 1759–1768. [[http://genome.cshlp.org/content/27/10/1759.long link]] [[https://www.ncbi.nlm.nih.gov/pubmed/28855263 PubMed]]
  
Line 11: Line 14:
 
==== Intron retention analysis ====
 
==== Intron retention analysis ====
 
* Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipahani, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. ''Genome Research'', 24:1774-86. [[http://genome.cshlp.org/content/early/2014/09/24/gr.177790.114 link]] [[http://www.ncbi.nlm.nih.gov/pubmed/25258385 PubMed]]
 
* Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipahani, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. ''Genome Research'', 24:1774-86. [[http://genome.cshlp.org/content/early/2014/09/24/gr.177790.114 link]] [[http://www.ncbi.nlm.nih.gov/pubmed/25258385 PubMed]]
−
 
−
==== DATABASES FOR OTHER SPECIES  ====
 
−
==== Chicken ====
 
−
* Gueroussov, S., Gonatopoulos-Pournatzis, T., Irimia, M., Raj, B., Lin, Z.Y., Gingras, A.C., Blencowe, B.J. (2015). An alternative splicing event amplifies evolutionary differences between vertebrates. ''Science'', 349:868-73. [[http://science.sciencemag.org/content/349/6250/868 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/26293963 PubMed]]
 
−
 
−
==== Zebrafish ====
 
−
* Burguera, D., Marquez, Y., Racioppi, C., Permanyer, J., Torres-Mendez, T., Esposito, R., Albuixech, B., Fanlo, L., D'Agostino, Y., Gohr, A., Navas-Perez, E., Riesgo, A., Cuomo, C., Benvenuto, G., Christiaen, L.A., Martí, E., D'Aniello, S., Spagnuolo, A., Ristoratore, F., Arnone, M.I., Garcia-Fernàndez, J., Irimia, M. (2017). Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes. ''Nat Commun'', 8:1799. [[https://www.nature.com/articles/s41467-017-01961-y link]] [[https://www.ncbi.nlm.nih.gov/pubmed/29180615 Pubmed]]
 
−
 
−
==== Amphioxus ====
 
−
* Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701. [[https://www.nature.com/articles/s41559-019-0813-6 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/30833759 PubMed]]
 
−
 
−
==== Sea Urchin ====
 
−
* Burguera, D., Marquez, Y., Racioppi, C., Permanyer, J., Torres-Mendez, T., Esposito, R., Albuixech, B., Fanlo, L., D'Agostino, Y., Gohr, A., Navas-Perez, E., Riesgo, A., Cuomo, C., Benvenuto, G., Christiaen, L.A., Martí, E., D'Aniello, S., Spagnuolo, A., Ristoratore, F., Arnone, M.I., Garcia-Fernàndez, J., Irimia, M. (2017). Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes. ''Nat Commun'', 8:1799. [[https://www.nature.com/articles/s41467-017-01961-y link]] [[https://www.ncbi.nlm.nih.gov/pubmed/29180615 Pubmed]]
 
−
 
−
==== Drosophila ====
 
−
* Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701. [[https://www.nature.com/articles/s41559-019-0813-6 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/30833759 PubMed]]
 
−
 
−
==== Centipede ====
 
−
* Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701. [[https://www.nature.com/articles/s41559-019-0813-6 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/30833759 PubMed]]
 
−
 
−
==== Planarian ====
 
−
* Solana, J., Irimia, M., Ayoub, S., Orejuela, M.R., Zywitza, V., Jens, M., Tapial, J., Ray, D., Morris, Q.D., Hughes, T.R., Blencowe, B.J., Rajewsky, N. (2016). Conserved functional antagonism between CELF and MBNL proteins regulates stem cell-specific alternative splicing and regeneration in planarians. Elife, 5:e16797. [[https://elifesciences.org/articles/16797 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/27502555 PubMed]]
 
−
 
−
==== Sea Anemone ====
 
−
* Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701. [[https://www.nature.com/articles/s41559-019-0813-6 link]] [[https://www.ncbi.nlm.nih.gov/pubmed/30833759 PubMed]]
 

Revision as of 13:44, 22 June 2020


PastDB publication

  • Martin, G., Marquez, Y., Duque, P., Irimia, M. (2020). Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions reveal major differences with animals. In preparation.

VastDB publication (v1.0)

  • Tapial, J., Ha, K. C. H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B. J., Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Research, 27(10), 1759–1768. [link] [PubMed]

vast-tools

  • Tapial, J., Ha, K. C. H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayon, T., Manzanares, M., Ponomarenko, J., Blencowe, B. J., Irimia, M. (2017). An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms. Genome Research, 27(10), 1759–1768. [link] [PubMed]
  • Irimia, M., Weatheritt, R.J., Ellis, J., Parikshak, N.N., Gonatopoulos-Pournatzis, T., Babor, M., Quesnel-Vallières, M., Tapial, J., Raj, B., O’Hanlon, D., Barrios-Rodiles, M., Sternberg, M.J.E., Cordes, S.P., Roth, F.P., Wrana, J.L., Geschwind, D.H., Blencowe, B.J. (2014). A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell, 59:1511-23. [link] [PubMed]

Intron retention analysis

  • Braunschweig, U., Barbosa-Morais, N.L., Pan, Q., Nachman, E., Alipahani, B., Gonatopoulos-Pournatzis, T., Frey, B., Irimia, M., Blencowe, B.J. (2014). Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research, 24:1774-86. [link] [PubMed]
Retrieved from "http://pastdb.crg.eu/w/index.php?title=Publications&oldid=324"