Highlighted Articles
Huang X, Rymbekova A, Dolgova O, Lao O, Kuhlwilm M. Harnessing deep learning for population genetic inference. Nat Rev Genet. 2024 Jan;25(1):61-78. doi:10.1038/s41576-023-00636-3. Epub 2023 Sep 4. PMID: 37666948. Integrative Genomics Lab
Jabalera Y, Tascón I, Samperio S, López-Alonso JP, Gonzalez-Lopez M, Aransay AM, Abascal-Palacios G, Beisel CL, Ubarretxena-Belandia I, Perez-Jimenez R. A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection. Nat Biotechnol. 2024 Oct 31. doi: 10.1038/s41587-024-02461-3. Epub ahead of print. PMID: 39482449. Synthetic Biology Lab & Genomic Analysis Platform
Fan W, Cao D, Yang B, Wang J, Li X, Kitka D, Li TWH, You S, Shiao S, Gangi A, Posadas E, Di Vizio D, Tomasi ML, Seki E, Mato JM, Yang H, Lu SC. Hepatic prohibitin 1 and methionine adenosyltransferase α1 defend against primary and secondary liver cancer metastasis. J Hepatol. 2024 Mar;80(3):443-453. doi: 10.1016/j.jhep.2023.11.022. Epub 2023 Dec 10. PMID: 38086446; PMCID: PMC10922446. Precision Medicine and Metabolism Lab
Grännö O, Bergemalm D, Salomon B, Lindqvist CM, Hedin CRH, Carlson M, Dannenberg K, Andersson E, Keita ÅV, Magnusson MK, Eriksson C, Lanka V; BIOIBD consortium; Magnusson PKE, D’Amato M, Öhman L, Söderholm JD, Hultdin J, Kruse R, Cao Y, Repsilber D, Grip O, Karling P, Halfvarson J. Preclinical Protein Signatures of Crohn’s Disease and Ulcerative Colitis: A Nested Case-Control Study Within Large Population-Based Cohorts. Gastroenterology. 2025 Apr;168(4):741-753. doi: 10.1053/j.gastro.2024.11.006. Epub 2024 Nov 26. PMID:39608683. Gastrointestinal Genetics Lab
Breitkopf-Heinlein K, Martinez-Chantar ML. Targeting hepatic stellate cells to combat liver fibrosis: where do we stand? Gut. 2024 Aug 8;73(9):1411-1413. doi: 10.1136/gutjnl-2023-331785. PMID: 38684236. Liver Disease Lab
Thompson AJ, Wu NC, Canales A, Kikuchi C, Zhu X, de Toro BF, Cañada FJ, Worth C, Wang S, McBride R, Peng W, Nycholat CM, Jiménez-Barbero J, Wilson IA, Paulson JC. Evolution of human H3N2 influenza virus receptor specificity has substantially expanded the receptor-binding domain site. Cell Host Microbe. 2024 Feb 14;32(2):261-275.e4. doi: 10.1016/j.chom.2024.01.003. Epub 2024 Feb 1. PMID: 38307019; PMCID: PMC11057904. Chemical Glycobiology Lab
Vacca M, Kamzolas I, Harder LM, Oakley F, Trautwein C, Hatting M, Ross T, Bernardo B, Oldenburger A, Hjuler ST, Ksiazek I, Lindén D, Schuppan D, Rodriguez-Cuenca S, Tonini MM, Castañeda TR, Kannt A, Rodrigues CMP, Cockell S, Govaere O, Daly AK, Allison M, Honnens de Lichtenberg K, Kim YO, Lindblom A, Oldham S, Andréasson AC, Schlerman F, Marioneaux J, Sanyal A, Afonso MB, Younes R, Amano Y, Friedman SL, Wang S, Bhattacharya D, Simon E, Paradis V, Burt A, Grypari IM, Davies S, Driessen A, Yashiro H, Pors S, Worm Andersen M, Feigh M, Yunis C, Bedossa P, Stewart M, Cater HL, Wells S, Schattenberg JM, Anstee QM; LITMUS Investigators; Tiniakos D, Perfield JW, Petsalaki E, Davidsen P, Vidal- Puig A. An unbiased ranking of murine dietary models based on their proximity to human metabolic dysfunction-associated steatotic liver disease (MASLD).Litmus Investigators: Millet O, Mato JM Nat Metab. 2024 Jun;6(6):1178-1196. doi: 10.1038/s42255-024-01043-6. Epub 2024 Jun 12. PMID: 38867022; PMCID: PMC11199145. Precision Medicine and Metabolism Lab
Baños-Jaime B, Corrales-Guerrero L, Pérez-Mejías G, Rejano-Gordillo CM, Velázquez-Campoy A, Martínez-Cruz LA, Martínez-Chantar ML, De la Rosa MA, Díaz-Moreno I. Phosphorylation at the disordered N-end makes HuR accumulate and dimerize in the cytoplasm. Nucleic Acids Res. 2024 Aug 12;52(14):8552-8565. doi: 10.1093/nar/gkae564. PMID: 38966993; PMCID: PMC11317137. Liver Disease Lab
Lin PH, Xu Y, Bali SK, Kim J, Gimeno A, Roberts ET, James D, Almeida NMS, Loganathan N, Fan F, Wilson AK, Jonathan Amster I, Moremen KW, Liu J, Jiménez- Barbero J, Huang X. Solid-Phase-Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides. Angew Chem Int Ed Engl. 2024 Aug 19;63(34):e202405671. doi: 10.1002/anie.202405671. Epub 2024 Jul 11. PMID: 38781001; PMCID: PMC11772155. Chemical Glycobiology Lab
Palviainen M, Puutio J, Østergaard RH, Eble JA, Maaninka K, Butt U, Ndika J, Kari OK, Kamali-Moghaddam M, Kjaer-Sorensen K, Oxvig C, Aransay AM, Falcon-Perez JM, Federico A, Greco D, Laitinen S, Hayashi Y, Siljander PR. Beyond basic characterization and omics: Immunomodulatory roles of platelet-derived extracellular vesicles unveiled by functional testing. J Extracell Vesicles. 2024 Oct;13(10):e12513. doi: 10.1002/jev2.12513. Erratum in: J Extracell Vesicles. 2024 Dec;13(12):e70015. doi: 10.1002/jev2.700 15. PMID: 39330919; PMCID: PMC11428872. Exosomes Lab & Genomic Analysis Platform
Welsh JA, Goberdhan DCI, O’Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon-Perez JM, Fu QL, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic-Talisman T, Kruh-Garcia NA, Ku’ulei-Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens-Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter-Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ; MISEV Consortium;Théry C, Witwer KW. Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles. 2024 Feb;13(2):e12404. doi: 10.1002/jev2.12404. Erratum in: J Extracell Vesicles. 2024 May;13(5):e12451. doi: 10.1002/jev2.12451. PMID: 38326288; PMCID: PMC10850029. Exosomes Lab
Sandau US, Magaña SM, Costa J, Nolan JP, Ikezu T, Vella LJ, Jackson HK, Moreira LR, Palacio PL, Hill AF, Quinn JF, Van Keuren-Jensen KR, McFarland TJ, Palade J, Sribnick EA, Su H, Vekrellis K, Coyle B, Yang Y, Falcón-Perez JM, Nieuwland R, Saugstad JA; International Society for Extracellular Vesicles Cerebrospinal Fluid Task Force. Recommendations for reproducibility of cerebrospinal fluid extracellular vesicle studies. J Extracell Vesicles. 2024 Jan;13(1):e12397. doi: 10.1002/jev2.12397. Erratum in: J Extracell Vesicles. 2024 Jan;13(1):e12405. doi: 10.1002/jev2.12405. PMID: 38158550; PMCID: PMC10756860. Exosomes Lab
Conduit SE, Pearce W, Bhamra A, Bilanges B, Bozal-Basterra L, Foukas LC, Cobbaut M, Castillo SD, Danesh MA, Adil M, Carracedo A, Graupera M, McDonald NQ, Parker PJ, Cutillas PR, Surinova S, Vanhaesebroeck B. A class I PI3K signalling network regulates primary cilia disassembly in normal physiology and disease. Nat Commun. 2024 Aug 21;15(1):7181. doi: 10.1038/s41467-024-51354-1. PMID: 39168978; PMCID: PMC11339396. Cancer Cell Signaling And Metabolism Lab
Salihovic S, Nyström N, Mathisen CB, Kruse R, Olbjørn C, Andersen S, Noble AJ, Dorn-Rasmussen M, Bazov I, Perminow G, Opheim R, Detlie TE, Huppertz-Hauss G, Hedin CRH, Carlson M, Öhman L, Magnusson MK, Keita ÅV, Söderholm JD, D’Amato M, Orešič M, Wewer V, Satsangi J, Lindqvist CM, Burisch J, Uhlig HH, Repsilber D, Hyötyläinen T, Høivik ML, Halfvarson J. Identification and validation of a blood- based diagnostic lipidomic signature of pediatric inflammatory bowel disease. Nat Commun. 2024 Jun 3;15(1):4567. doi: 10.1038/s41467-024-48763-7. PMID: 38830848; PMCID: PMC11148148. Gastrointestinal Genetics Lab
Unione L, Ammerlaan ANA, Bosman GP, Uslu E, Liang R, Broszeit F, van der Woude R, Liu Y, Ma S, Liu L, Gómez-Redondo M, Bermejo IA, Valverde P, Diercks T, Ardá A, de Vries RP, Boons GJ. Probing altered receptor specificities of antigenically drifting human H3N2 viruses by chemoenzymatic synthesis, NMR, and modeling. Nat Commun. 2024 Apr 6;15(1):2979. doi: 10.1038/s41467-024-47344-y. PMID: 38582892; PMC10998905. Chemical Glycobiology Lab & NMR Platform
Spencer RKW, Santos-Pérez I, Rodríguez-Renovales I, Martinez Galvez JM, Shnyrova AV, Müller M. Membrane fission via transmembrane contact. Nat Commun. 2024 Mar 30;15(1):2793. doi: 10.1038/s41467-024-47122-w. PMID: 38555357; PMCID: PMC10981662. Electron Microscopy and Macromolecular Crystallography Platforms
Eraña H, Sampedro-Torres-Quevedo C, Charco JM, Díaz-Domínguez CM, Peccati F, San-Juan-Ansoleaga M, Vidal E, Gonçalves-Anjo N, Pérez-Castro MA, González- Miranda E, Piñeiro P, Fernández-Veiga L, Galarza-Ahumada J, Fernández-Muñoz E, Perez de Nanclares G, Telling G, Geijo M, Jiménez-Osés G, Castilla J. A Protein Misfolding Shaking Amplification-based method for the spontaneous generation of hundreds of bona fide prions. Nat Commun. 2024 Mar 8;15(1):2112. doi: 10.1038/s41467-024-46360-2. PMID: 38459071; PMCID: PMC10923866. Computational Chemistry Lab & Prion Research Lab
Pérez-Jover I, Rochon K, Hu D, Mahajan M, Madan Mohan P, Santos-Pérez I, Ormaetxea Gisasola J, Martinez Galvez JM, Agirre J, Qi X, Mears JA, Shnyrova AV, Ramachandran R. Allosteric control of dynamin-related protein 1 through a disordered C-terminal Short Linear Motif. Nat Commun. 2024 Jan 2;15(1):52. doi: 10.1038/s41467-023-44413-6. PMID: 38168038; PMCID: PMC10761769. Electron Microscopy and Macromolecular Crystallography Platforms
Armand M, Nin-Hill A, Ardá A, Berrino E, Désiré J, Martin-Mingot A, Michelet B, Jiménez-Barbero J, Blériot Y, Rovira C, Thibaudeau S. Glycosylium Ions in Superacid Mimic the Transition State of Enzyme Reactions. J Am Chem Soc. 2024 Nov 27;146(47):32618-32626. doi: 10.1021/jacs.4c11677. Epub 2024 Nov 13. PMID: 39535973.. Chemical Glycobiology Lab
Unnikrishnan VB, Sabatino V, Amorim F, Estrada MF, Navo CD, Jimenez-Oses G, Fior R, Bernardes GJL. Gold(III)-Induced Amide Bond Cleavage In Vivo: A Dual Release Strategy via π-Acid Mediated Allyl Substitution. J Am Chem Soc. 2024 Aug 21;146(33):23240-23251. doi: 10.1021/jacs.4c05582. Epub 2024 Aug 7. PMID: 39113488; PMCID: PMC11345771.Computational Chemistry Lab
Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation. J Am Chem Soc. 2024 May 22;146(20):14328-14340. doi: 10.1021/jacs.4c03994. Epub 2024 May 10. PMID: 38728535; PMCID: PMC11225102.Computational Chemistry Lab
Sumida KH, Núñez-Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, Dauparas J, Wang J, Kipnis Y, Jameson N, Kang A, De La Cruz J, Sankaran B, Bera AK, Jiménez-Osés G, Baker D. Improving Protein Expression, Stability, and Function with ProteinMPNN. J Am Chem Soc. 2024 Jan 24;146(3):2054-2061. doi: 10.1021/jacs.3c10941. Epub 2024 Jan 9. PMID: 38194293; PMCID: PMC10811672.Computational Chemistry Lab
Yadav N, Djalali S, Poveda A, Ricardo MG, Seeberger PH, Jiménez-Barbero J, Delbianco M. Dissecting the Conformational Stability of a Glycan Hairpin. J Am Chem Soc. 2024 Mar 6;146(9):6369-6376. doi: 10.1021/jacs.4c00423. Epub 2024 Feb PMID: 38377472; PMCID: PMC10921397.Chemical Glycobiology Lab
O’Shea JM, Yun YJ, Jamhawi AM, Peccati F, Jiménez-Osés G, Ayitou AJ. Doublet Spin State Mediated Photoluminescence Upconversion in Organic Radical Donor- Triplet Acceptor Dyads. J Am Chem Soc. 2025 Jan 8;147(1):1017-1027. doi: 10.1021/jacs.4c14303. Epub 2024 Dec 19. PMID: 39698846.. Computational Chemistry Lab
Gimeno A, Ehlers AM, Delgado S, Langenbach JH, van den Bos LJ, Kruijtzer JAW, Guigas BGA, Boons GJ. Site-Specific Glyco-Tagging of Native Proteins for the Development of Biologicals. J Am Chem Soc. 2024 Dec 18;146(50):34452-34465. doi: 10.1021/jacs.4c11091. Epub 2024 Dec 9. PMID: 39653378; PMCID: PMC11664507. Chemical Glycobiology Lab
Corres-Mendizabal J, Zacchi F, Martín-Martín N, Mateo J, Carracedo A. Metastatic hormone-naïve prostate cancer: a distinct biological entity. Trends Cancer. 2024 Sep;10(9):825-841. doi: 10.1016/j.trecan.2024.06.005. Epub 2024 Jul 23 PMID: 39048488; PMCID: PMC11397905.Cancer Cell Signaling And Metabolism Lab
Nonne F, Iacono LD, Bertuzzi S, Unione L, Proietti D, Norais N, Margarit I, Adamo R, Jiménez-Barbero J, Carboni F, Romano MR. A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope. ACS Cent Sci. 2024 Feb 22;10(5):978-987. doi: 10.1021/acscentsci.3c01515. PMID: 38799664; PMCID: PMC11117310.. Chemical Glycobiology Lab
Patsch D, Schwander T, Voss M, Schaub D, Hüppi S, Eichenberger M, Stockinger P, Schelbert L, Giger S, Peccati F, Jiménez-Osés G, Mutný M, Krause A, Bornscheuer UT, Hilvert D, Buller RM. Enriching productive mutational paths accelerates enzyme evolution. Nat Chem Biol. 2024 Dec;20(12):1662-1669. doi: 10.1038/s41589-024-01712-3. Epub 2024 Sep 11. PMID: 39261644; PMCID: PMC11581979.Computational Chemistry Lab
Noureddin M, Truong E, Mayo R, Martínez-Arranz I, Mincholé I, Banales JM, Arrese M, Cusi K, Arias-Loste MT, Bruha R, Romero-Gómez M, Iruzubieta P, Aller R, Ampuero J, Calleja JL, Ibañez-Samaniego L, Aspichueta P, Martín-Duce A, Kushner T, Ortiz P, Harrison SA, Anstee QM, Crespo J, Mato JM, Sanyal AJ. Serum identification of at-risk MASH: The metabolomics-advanced steatohepatitis fibrosis score (MASEF). Hepatology. 2024 Jan 1;79(1):135-148. doi: 10.1097/HEP.0000000000000542. Epub 2023 Jul 24. PMID: 37505221; PMCID: PMC10718221.Liver Disease Lab
González-Recio I, Goikoetxea-Usandizaga N, Rejano-Gordillo CM, Conter C, Rodríguez Agudo R, Serrano-Maciá M, Zapata-Pavas LE, Peña-Sanfélix P, Azkargorta M, Elortza F, Herranz JM, Guillamon Thiery Á, Guerra-Ruiz AR, Jover R, Galicia-Garcia U, Martín C, Schaeper U, Delgado TC, Díaz-Moreno I, Díaz Quintana A, Buccella D, Nogueiras R, Argemi J, Ávila MA, Gratacós-Ginès J, Iruzubieta P, Pose E, Bataller R, Crespo J, Martínez-Cruz LA, Martínez-Chantar ML. Modulatory effects of CNNM4 on protein- l -isoaspartyl- O -methyltransferase repair function during alcohol-induced hepatic damage. Hepatology. 2024 Nov 19. doi: 10.1097/HEP.0000000000001156. Epub ahead of print. PMID: 39641635. Liver Disease Lab
Patsch D, Schwander T, Voss M, Schaub D, Hüppi S, Eichenberger M, Stockinger P, Schelbert L, Giger S, Peccati F, Jiménez-Osés G, Mutný M, Krause A, Bornscheuer UT, Hilvert D, Buller RM. Enriching productive mutational paths accelerates enzyme evolution. Nat Chem Biol. 2024 Dec;20(12):1662-1669. doi: 10.1038/s41589-024-01712-3. Epub 2024 Sep 11. PMID: 39261644; PMCID: PMC11581979. iComputational Chemistry Lab
Iriondo O, Mecenas D, Li Y, Chin CR, Thomas A, Moriarty A, Marker R, Wang YJ, Hendrick H, Amzaleg Y, Ortiz V, MacKay M, Dickerson A, Lee G, Harotoonian S, Benayoun BA, Smith A, Mason CE, Roussos Torres ET, Klotz R, Yu M. Hypoxic Memory Mediates Prolonged Tumor-Intrinsic Type I Interferon Suppression to Promote Breast Cancer Progression. Cancer Res. 2024 Oct 1;84(19):3141-3157. doi: 10.1158/0008-5472.CAN-23-2028. PMID: 38990731; PMCID: PMC11444891. Cancer Cell Signaling And Metabolism Lab
Castelo J, Araujo-Aris S, Barriales D, Tanner Pasco S, Seoane I, Peña-Cearra A, Palacios A, Simó C, Garcia-Cañas V, Khamwong M, Martín-Ruiz I, Gonzalez-Lopez M, Barcena L, Martín Rodríguez JE, Lavín JL, Gutiez N, Marcos R, Atondo E, Cobela A, Plaza-Vinuesa L, Plata A, Santos-Fernandez E, Fernandez-Tejada A, Villarán MC, Mancheño JM, Maria Flores J, María Aransay A, Pellón A, de Las Rivas B, Muñoz R, Margolles A, Ruas-Madiedo P, Victoria Selma M, Gomez de Agüero M, Abecia L, Anguita J, Rodríguez H. The microbiota metabolite, phloroglucinol, confers long-term protection against inflammation. Gut Microbes. 2024 Jan-Dec;16(1):2438829. doi: 10.1080/19490976.2024.2438829. Epub 2024 Dec 15. PMID: 39676480; PMCID: PMC11651279. Inflammation and Macrophage Plasticity Lab
Iruzubieta P, Damborenea A, Ioghen M, Bajew S, Fernandez-Torrón R, Töpf A, Herrero-Reiriz Á, Epure D, Vill K, Hernández-Laín A, Manterola M, Azkargorta M, Pikatza-Menoio O, Pérez-Fernandez L, García-Puga M, Gaina G, Bastian A, Streata I, Walter MC, Müller-Felber W, Thiele S, Moragón S, Bastida-Lertxundi N, López- Cortajarena A, Elortza F, Gereñu G, Alonso-Martin S, Straub V, de Sancho D, Teleanu R, López de Munain A, Blázquez L. Biallelic variants in SNUPN cause a limb girdle muscular dystrophy with myofibrillar-like features. Brain. 2024 Aug 1;147(8):2867-2883. doi: 10.1093/brain/awae046. PMID: 38366623; PMCID: PMC11292911. Proteomics Platform
Brandi, J, Siragusa, G, Robotti, E, Marengo, E, Cecconi, D. Analysis of veterinary drugs and pesticides in food using liquid chromatography-mass spectrometry. Trac-trends in analytical Chemistry. Volume: 179. Issue: . Pages: -. DOI: 10.1016/j.trac.2024.117888. Date: 2024-07-26. Cancer Heterogeneity Lab