diff --git a/content/en/publications/2021.md b/content/en/publications/2021.md index cb5555e..c681099 100644 --- a/content/en/publications/2021.md +++ b/content/en/publications/2021.md @@ -90,7 +90,8 @@ PMID: [33800656](https://pubmed.ncbi.nlm.nih.gov/33800656/) #### Short and dysfunctional telomeres sensitize the kidneys to develop fibrosis. Saraswati, S., Martínez, P., **Graña-Castro, O.** Blasco M.A. -***Nat Aging 1***, 269–283 (2021). doi: 10.1038/s43587-021-00040-8. [37118410](https://pubmed.ncbi.nlm.nih.gov/37118410/) +***Nat Aging 1***, 269–283 (2021). doi: 10.1038/s43587-021-00040-8. +PMID: [37118410](https://pubmed.ncbi.nlm.nih.gov/37118410/) #### Association between BRCA2 alterations and intraductal and cribriform histologies in prostate cancer. Lozano R, Salles D.C, Shahneen S, Aragón M.I, Thorne H, López-Campos F, Rubio-Briones J, Gutierrez-Pecharroman M.A, Maldonado L, **Di Domenico T**, Sanz A, Prieto J.D, García I, Pacheco I.M, Garcés T, Llacer C, Romero-Laorden N, Zambrana F, López-Casas P.P, Llorente D, Mateo J, Pritchard C.C, Antonarakis S.E, Olmos D, Lotan L.T, Castro E. diff --git a/content/en/publications/2024.md b/content/en/publications/2024.md index 48a2b64..e6d9303 100644 --- a/content/en/publications/2024.md +++ b/content/en/publications/2024.md @@ -15,44 +15,69 @@ hero: autonumbering: true --- +#### The rapid degradation of translated upstream regions points to an inefficient translation initiation process +**Tress ML**. +***bioRxiv*** [Preprint]. 2024 Nov 25. doi: 10.1101/2024.11.25.625198 +[Link](https://doi.org/10.1101/2024.11.25.625198) + +#### GENCODE 2025: reference gene annotation for human and mouse +Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, **Cerdán-Vélez D**, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, **Maquedano M**, Gómez LM, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, **Tress ML**, Birney E, Martin FJ, Frankish A. +***Nucleic Acids Res***. 2024 Nov 20:gkae1078. doi: 10.1093/nar/gkae1078. Epub ahead of print. +PMID: [39565199](https://pubmed.ncbi.nlm.nih.gov/39565199/) + +#### A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation +Rodriguez JM, **Maquedano M**, **Cerdan-Velez D**, Calvo E, Vazquez J, **Tress ML**. +***bioRxiv*** [Preprint]. 2024 Nov 15:2024.11.14.623419. doi: 10.1101/2024.11.14.623419. +PMID: [39605392](https://pubmed.ncbi.nlm.nih.gov/39605392/) + +#### GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing +Kaur G, Perteghella T, Carbonell-Sala S, Gonzalez-Martinez J, Hunt T, Mądry T, Jungreis I, Arnan C, Lagarde J, Borsari B, Sisu C, Jiang Y, Bennett R, Berry A, **Cerdán-Vélez D**, Cochran K, Vara C, Davidson C, Donaldson S, Dursun C, González-López S, Gopal Das S, Hardy M, Hollis Z, Kay M, Montañés JC, Ni P, Nurtdinov R, Palumbo E, Pulido-Quetglas C, Suner MM, Yu X, Zhang D, Loveland JE, Albà MM, Diekhans M, Tanzer A, Mudge JM, Flicek P, Martin FJ, Gerstein M, Kellis M, Kundaje A, Paten B, **Tress ML**, Johnson R, Uszczynska-Ratajczak B, Frankish A, Guigó R. +***bioRxiv*** [Preprint]. 2024 Oct 31:2024.10.29.620654. doi: 10.1101/2024.10.29.620654. +PMID: [39554180](https://pubmed.ncbi.nlm.nih.gov/39554180/) + #### TIMP1 mediates astrocyte-dependent local immunosuppression in brain metastasis acting on infiltrating CD8+ T cells Priego N, de Pablos-Aragoneses A, Perea-García M, Pieri V, Hernandez-Oliver C, Alvaro-Espinosa L, Rojas A, Sanchez O, Steindl A, Caleiras E, Garcia F, **Garcia-Martin S**, **Grana-Castro O**, Garcia-Mulero S, Serrano D, Velasco-Beltran P, Jimenez-Lasheras B, Egia-Mendikute L, Rupp L, Stammberger A, Meinhardt M, Chaachou-Charradi A, Martínez-Saez E, Bertero L, Cassoni P, Mangherini L, Pellerino A, Ruda R, Soffietti R, **Al-Shahrour F**, Saftig P, Sanz-Pamplona R, Schmitz M, Crocker SJ, Calvo A, Palazon A, Group R, Valiente M. -**Cancer Discov**. 2024 Oct 2. doi: 10.1158/2159-8290.CD-24-0134. Epub ahead of print. +***Cancer Discov***. 2024 Oct 2. doi: 10.1158/2159-8290.CD-24-0134. Epub ahead of print. PMID: [39354883](https://pubmed.ncbi.nlm.nih.gov/39354883/) #### Renal fibroblasts are involved in fibrogenic changes in kidney fibrosis associated with dysfunctional telomeres Saraswati S, Martínez P, Serrano R, Mejías D, **Graña-Castro O**, **Álvarez Díaz R**, Blasco MA. -**Exp Mol Med**. 2024 Oct 1. doi: 10.1038/s12276-024-01318-8. Epub ahead of print. +***Exp Mol Med***. 2024 Oct 1. doi: 10.1038/s12276-024-01318-8. Epub ahead of print. PMID: [39349834](https://pubmed.ncbi.nlm.nih.gov/39349834/) #### MAML3-fusions modulate vascular and immune tumour microenvironment and confer high metastatic risk in pheochromocytoma and paraganglioma Monteagudo M, Calsina B, Salazar-Hidalgo ME, Martínez-Montes ÁM, **Piñeiro-Yáñez E**, Caleiras E, Martín MC, Rodríguez-Perales S, Letón R, Gil E, Buffet A, Burnichon N, Fernández-Sanromán Á, Díaz-Talavera A, Mellid S, Arroba E, Reglero C, Martínez-Puente N, Roncador G, Del Olmo MI, Corrales PJP, Oliveira CL, Álvarez-Escolá C, Gutiérrez MC, López-Fernández A, García NP, Regojo RM, Díaz LR, Laorden NR, Guadarrama OS, Bechmann N, Beuschlein F, Canu L, Eisenhofer G, Fassnacht M, Nölting S, Quinkler M, Rapizzi E, Remde H, Timmers HJ, Favier J, Gimenez-Roqueplo AP, Rodriguez-Antona C, Currás-Freixes M, **Al-Shahrour F**, Cascón A, Leandro-García LJ, Montero-Conde C, Robledo M. -**Best Pract Res Clin Endocrinol Metab**. 2024 Aug 29:101931. doi: 10.1016/j.beem.2024.101931. Epub ahead of print. +***Best Pract Res Clin Endocrinol Metab***. 2024 Aug 29:101931. doi: 10.1016/j.beem.2024.101931. Epub ahead of print. PMID: [39218714](https://pubmed.ncbi.nlm.nih.gov/39218714/) #### Type I interferon signaling pathway enhances immune-checkpoint inhibition in KRAS mutant lung tumors Fernández-García F, Fernández-Rodríguez A, **Fustero-Torre C**, **Piñeiro-Yáñez E**, Wang H, Lechuga CG, Callejas S, Álvarez R, López-García A, Esteban-Burgos L, Salmón M, San Román M, Guerra C, Ambrogio C, Drosten M, Santamaría D, **Al-Shahrour F**, Dopazo A, Barbacid M, Musteanu M. -**Proc Natl Acad Sci U S A**. 2024 Sep 3;121(36):e2402913121. doi: 10.1073/pnas.2402913121. Epub 2024 Aug 26. +***Proc Natl Acad Sci U S A***. 2024 Sep 3;121(36):e2402913121. doi: 10.1073/pnas.2402913121. Epub 2024 Aug 26. PMID: [39186651](https://pubmed.ncbi.nlm.nih.gov/39186651/) #### Evidence for widespread translation of 5' untranslated regions Rodriguez JM, Abascal F, **Cerdán-Vélez D**, Gómez LM, Vázquez J, **Tress ML**. -**Nucleic Acids Res**. 2024 Aug 12;52(14):8112-8126. doi: 10.1093/nar/gkae571. +***Nucleic Acids Res***. 2024 Aug 12;52(14):8112-8126. doi: 10.1093/nar/gkae571. PMID: [38953162](https://pubmed.ncbi.nlm.nih.gov/38953162/) +#### A mild increase in nutrient signaling to mTORC1 in mice leads to parenchymal damage, myeloid inflammation and shortened lifespan +Ortega-Molina A, Lebrero-Fernández C, Sanz A, Calvo-Rubio M, Deleyto-Seldas N, de Prado-Rivas L, Plata-Gómez AB, Fernández-Florido E, González-García P, Vivas-García Y, Sánchez García E, **Graña-Castro O**, Price NL, Aroca-Crevillén A, Caleiras E, Monleón D, Borrás C, Casanova-Acebes M, de Cabo R, Efeyan A. +***Nat Aging***. 2024 Aug;4(8):1102-1120. doi: 10.1038/s43587-024-00635-x. Epub 2024 Jun 7. +PMID: [38849535](https://pubmed.ncbi.nlm.nih.gov/38849535/) + #### The 1+Million Genomes Minimal Dataset for Cancer Riba M, Sala C, Culhane AC, Flobak Å, Patocs A, Boye K, Plevova K, Pospíšilová Š, Gandolfi G, Morelli MJ, Bucci G, Edsjö A, Lassen U, **Al-Shahrour F**, Lopez-Bigas N, Hovland R, Cuppen E, Valencia A, Poirel HA, Rosenquist R, Scollen S, Arenas Marquez J, Belien J, De Nicolo A, De Maria R, Torrents D, Tonon G. -**Nat Genet**. 2024 May;56(5):733-736. doi: 10.1038/s41588-024-01721-x. +***Nat Genet***. 2024 May;56(5):733-736. doi: 10.1038/s41588-024-01721-x. PMID: [38702538](https://pubmed.ncbi.nlm.nih.gov/38702538/) #### The Peptidoglycan Recognition Protein 1 confers immune evasive properties on pancreatic cancer stem cells López-Gil JC, García-Silva S, Ruiz-Cañas L, Navarro D, Palencia-Campos A, Giráldez-Trujillo A, Earl J, Dorado J, **Gómez-López G**, Monfort-Vengut A, Alcalá S, Gaida MM, García-Mulero S, Cabezas-Sáinz P, Batres-Ramos S, Barreto E, Sánchez-Tomero P, Vallespinós M, Ambler L, Lin ML, Aicher A, García García de Paredes A, de la Pinta C, Sanjuanbenito A, Ruz-Caracuel I, Rodríguez-Garrote M, Guerra C, Carrato A, de Cárcer G, Sánchez L, Nombela-Arrieta C, Espinet E, Sanchez-Arevalo Lobo VJ, Heeschen C, Sainz B Jr. -**Gut**. 2024 May 16. doi: 10.1136/gutjnl-2023-330995. Epub ahead of print. +***Gut***. 2024 May 16. doi: 10.1136/gutjnl-2023-330995. Epub ahead of print. PMID: [38754953](https://pubmed.ncbi.nlm.nih.gov/38754953/) #### Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver Plata-Gómez AB, de Prado-Rivas L, Sanz A, Deleyto-Seldas N, García F, de la Calle Arregui C, Silva C, Caleiras E, **Graña-Castro O**, **Piñeiro-Yáñez E**, Krebs J, Leiva-Vega L, Muñoz J, Jain A, Sabio G, Efeyan A. -**Nat Commun**. 2024 Mar 18;15(1):1878. doi: 10.1038/s41467-024-46032-1. +***Nat Commun***. 2024 Mar 18;15(1):1878. doi: 10.1038/s41467-024-46032-1. PMID: [38499523](https://pubmed.ncbi.nlm.nih.gov/38499523/) #### The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues @@ -73,4 +98,9 @@ PMID: [38321342](https://pubmed.ncbi.nlm.nih.gov/38321342/) #### The efficacy of chemotherapy is limited by intratumoral senescent cells expressing PD-L2 Chaib S, López-Domínguez JA, Lalinde-Gutiérrez M, Prats N, Marin I, Boix O, García-Garijo A, Meyer K, Muñoz MI, Aguilera M, Mateo L, Stephan-Otto Attolini C, Llanos S, Pérez-Ramos S, Escorihuela M, **Al-Shahrour F**, Cash TP, Tchkonia T, Kirkland JL, Abad M, Gros A, Arribas J, Serrano M. ***Nat Cancer***. 2024 Jan 24. doi: 10.1038/s43018-023-00712-x -PMID: [38267628](https://pubmed.ncbi.nlm.nih.gov/38267628/) \ No newline at end of file +PMID: [38267628](https://pubmed.ncbi.nlm.nih.gov/38267628/) + +#### Mammalian CDC14 phosphatases control exit from stemness in pluripotent cells +Villarroya-Beltri C, Martins AFB, García A, Giménez D, Zarzuela E, Novo M, Del Álamo C, González-Martínez J, Bonel-Pérez GC, Díaz I, Guillamot M, Chiesa M, Losada A, **Graña-Castro O**, Rovira M, Muñoz J, Salazar-Roa M, Malumbres M. +***EMBO J***. 2023 Jan 4;42(1):e111251. doi: 10.15252/embj.2022111251. Epub 2022 Nov 3. +PMID: [36326833](https://pubmed.ncbi.nlm.nih.gov/36326833/) \ No newline at end of file