More than 2,500 coding genes in the human reference gene set still have unsettled status
Maquedano M, Cerdán-Vélez D, Tress ML.
bioRxiv [Preprint]. 2024 Dec 05. doi: 10.1101/2024.12.05.626965
Link
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
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
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
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
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.
PMID: 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.
PMID: 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.
PMID: 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.
PMID: 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.
PMID: 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
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.
PMID: 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.
PMID: 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.
PMID: 38499523
The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues
Cerdán-Vélez D, Tress ML.
Bioinform Adv. 2024 Feb 28. doi: 10.1093/bioadv/vbae029
PMID: 38464973
A community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer
Mason M, Lapuente-Santana Ó, Halkola AS, Wang W, Mall R, Xiao X, Kaufman J, Fu J, Pfeil J, Banerjee J, Chung V, Chang H, Chasalow SD, Lin HY, Chai R, Yu T, Finotello F, Mirtti T, Mäyränpää MI, Bao J, Verschuren EW, Ahmed EI, Ceccarelli M, Miller LD, Monaco G, Hendrickx WRL, Sherif S, Yang L, Tang M, Gu SS, Zhang W, Zhang Y, Zeng Z, Das Sahu A, Liu Y, Yang W, Bedognetti D, Tang J, Eduati F, Laajala TD, Geese WJ, Guinney J, Szustakowski JD, Vincent BG, Carbone DP.
J Transl Med. 2024 Feb 21. doi: 10.1186/s12967-023-04705-3
PMID: 38383458
Roadmap for a European cancer data management and precision medicine infrastructure
Nikolski M, Hovig E, Al-Shahrour F, Blomberg N, Scollen S, Valencia A, Saunders G.
Nat Cancer. 2024 Feb 6. doi: 10.1038/s43018-023-00717-6
PMID: 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
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
