Department of Genetics Publications for November 2025

Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens. 

Adaptive immune response to West Nile virus infection in the Collaborative Cross mouse model: A database of cellular phenotypes and Quantitative Trait Loci. 

Chamberlin S, Graham J, Jeng S, Swarts J, Ferris M, Heise M, Baric RS, McWeeney S, Lund J, Mooney M.

Sci Data. 2025 Nov 21. doi: 10.1038/s41597-025-06293-x. Online ahead of print. PMID: 41271835

Cell type-specific inference from bulk RNA-sequencing data by integrating single-cell reference profiles via EPIC-unmix. 

Tang C, Sun Q, Zeng X, Li G, Yang X, Liu F, Zhao J, Shen Y, Liu B, Wen J, Li Y.

Genome Biol. 2025 Nov 20;26(1):395. doi: 10.1186/s13059-025-03847-5. PMID: 41267097 Free PMC article.

Inferring multi-organ genetic connections using imaging and clinical data through Mendelian randomization. 

Shu J, Zheng R, Chirinos J, Copana C, Li B, Fan Z, Yang X, Yang Y, Wang X, Li Y, Xi B, Li T, Zhu H, Zhao B.

Nat Biomed Eng. 2025 Nov 19. doi: 10.1038/s41551-025-01554-x. Online ahead of print. PMID: 41258051

RareLink: scalable REDCap-based framework for rare disease interoperability linking international registries to FHIR and Phenopackets. 

Graefe ASL, Rehburg F, Alkarkoukly S, Danis D, Grönke A, Hübner MR, Bartschke A, Debertshäuser T, Klopfenstein SAI, Saß J, Fleck J, Rehberg M, Zschüntzsch J, Nyoungui EF, Kalashnikova T, Murguía-Favela L, Derfalvi B, Wright NAM, Moosa S, Ogishima S, Semler O, Wiegand S, Kühnen P, Mungall CJ, Haendel MA, Robinson PN, Thun S, Beyan O.

NPJ Genom Med. 2025 Nov 18;10(1):72. doi: 10.1038/s41525-025-00534-z. PMID: 41253795 Free PMC article.

The missing link: electronic health record linkage across species offers opportunities for improving One Health. 

Mullen KR, Saklou N, Kiehl A, Ong TC, Strecker GJ, Toro S, VandeWoude S, Brooks IM, Webb TL, Haendel MA.

JAMIA Open. 2025 Nov 12;8(6):ooaf151. doi: 10.1093/jamiaopen/ooaf151. eCollection 2025 Dec. PMID: 41245152 Free PMC article.

Building a framework for reproducibility: the case for standardized data reporting and metadata integration in zebrafish research. 

Ngu MS, Toro S, Burger A, Ang KC.

Dis Model Mech. 2025 Nov 1;18(11):dmm052441. doi: 10.1242/dmm.052441. Epub 2025 Nov 18. PMID: 41250647

Federated double machine learning for high-dimensional semiparametric models. 

Kang K, Wu Z, Qian X, Song X, Zhu H.

Biometrics. 2025 Oct 8;81(4):ujaf150. doi: 10.1093/biomtc/ujaf150. PMID: 41268645

Evaluation and follow-up of newborns screening positive for mucopolysaccharidosis II: Results from an international modified Delphi consensus. 

Burton BK, Ellinwood NM, Hoffman KK, Muenzer J.

Mol Genet Metab. 2025 Nov 12;146(4):109285. doi: 10.1016/j.ymgme.2025.109285. Online ahead of print. PMID: 41265179

The offonome reveals on and off states of gene expression near the detection limit of RNA-seq. 

Choi WY, Zhao X, Holt J, Jain R, Jo H, Hoadley KA, Hayes DN, Choi HY.

Sci Rep. 2025 Nov 28. doi: 10.1038/s41598-025-27185-5. Online ahead of print. PMID: 41315666

Analysis of left ventricular mass for African American individuals using multi-ancestry polygenic risk scores: the Jackson Heart Study. 

McLaurin D, Turk P, Affuso O, Raffield LM, Heitman E.

Open Heart. 2025 Nov 27;12(2):e003501. doi: 10.1136/openhrt-2025-003501. PMID: 41314685

Menin-MLL1 complex cooperates with NF-Y to promote hepatocellular carcinoma survival. 

Dzama-Karels M, Sokolowski M, Kuhlers P, Brinkman JA, Morris JP 4th, Raab JR.

Cell Rep. 2025 Nov 25;44(12):116619. doi: 10.1016/j.celrep.2025.116619. Online ahead of print. PMID: 41296561

Identification of spirodioxolane nsP2 helicase inhibitors with antialphaviral activity. 

Oh HJ, Sears JD, Ramalingam BM, Saleem RSZ, Davis-Gilbert ZW, Hossain MA, Moorman SR, Ohja D, Martinez SA, Burdick JE, Couñago RM, Moorman NJ, Heise MT, Todd MH, Willson TM.

RSC Med Chem. 2025 Oct 31. doi: 10.1039/d5md00772k. Online ahead of print. PMID: 41292551 Free PMC article.

Association of metabolomics measurements with blood cell phenotypes. 

Chen BD, Tapia A, Boerwinkle E, Clish CB, Gerszten R, Graff M, Mohlke KL, Morrison AC, Pathmasiri W, Rich SS, Rotter JI, Rushing BR, Sumner S, Tracy RP, Young KL, Yu B, Thyagarajan B, Reiner AP, Li Y, Raffield L.

Blood Cells Mol Dis. 2025 Nov 4;117:102966. doi: 10.1016/j.bcmd.2025.102966. Online ahead of print. PMID: 41289847

Recommendations for responsible use of population descriptors in polygenic risk score development. 

Smith JL, Adebamowo CA, Adebamowo SN, Darst BF, Fullerton SM, Gogarten SM, Hamed ME, Hirbo JB, Hysong MR, Johar AS, Khan AT, Kullo IJ, Konigsberg IR, Kraft P, Lange LA, Li Y, Martin AR, Nelson SC, Choudhury A, Ramsay M, Cobran EK, Schaid DJ, Sharma J, Wang Y, Wojcik GL; Polygenic Risk Methods Development (PRIMED) Consortium; Sun Q.

Nat Genet. 2025 Nov 24. doi: 10.1038/s41588-025-02395-9. Online ahead of print. PMID: 41286102 Review.

Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation. 

Liu C, Joehanes R, Ma J, Xie J, Yang J, Wang M, Huan T, Hwang SJ, Wen J, Sun Q, Demirkale CY, Heard-Costa NL, Orchard P, Carson AP, Haessler JW, Raffield LM, Reiner AP, Franceschini N, Auer PL, Kooperberg C, Li Y, O’Connor G, Murabito JM, Munson P, Levy D.

Nat Commun. 2025 Nov 22;16(1):10615. doi: 10.1038/s41467-025-64336-8. PMID: 41274869 Free PMC article.

Investigating the neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies. 

Küry S, Stanton JE, van Woerden GM, Bosc-Rosati A, Hsieh TC, Bray L, Oloudé M, Rosenfelt C, Scott-Boyer MP, Most V, Wang T, Papendorf JJ, de Konink C, Deb W, Vignard V, Studencka-Turski M, Besnard T, Hajdukowicz AM, Thiel FG, Wolfgramm S, Florenceau L, Cuinat S, Marsac S, Verrès Y, Dangoumau A, Poirier L, Wentzensen IM, Tuttle A, Forster C, Striesow J, Golnik R, Ortiz D, Jenkins L, Rosenfeld JA, Ziegler A, Houdayer C, Bonneau D, Torti E, Begtrup A, Monaghan KG, Mullegama SV, Volker-Touw CMLN, van Gassen KLI, Oegema R, de Pagter MS, Steindl K, Rauch A, Ivanovski I, McDonald K, Boothe E, Dauber A, Baker J, Fabie NAV, Bernier RA, Turner TN, Srivastava S, Dies KA, Swanson LC, Costin C, Abdulrazak A, Jobling RK, Pappas J, Rabin R, Niyazov D, Chun-Hui Tsai A, Kovak K, Beck DB, Malicdan MCV, Adams DR, Wolfe L, Ganetzky RD, Muraresku CC, Babikyan D, Sedláček Z, Hančárová M, Timberlake AT, Saif HA, Nestler B, King K, Hajianpour MJ, Costain G, Prendergast D, Li C, Geneviève D, Vitobello A, Sorlin A, Philippe C, Harel T, Toker O, Sabir A, Lim D, Hamilton MJ, Bryson LJ, Cleary E, Weber S, Hoffman TL, Cueto-González AM, Tizzano EF, Gómez-Andrés D, Codina-Solà M, Ververi A, Pavlidou E, Lambropoulos A, Garganis K, Rio M, Levy J, Langas SJ, McRae AM, Lessard MK, D’Agostino MD, De Bie I, Wegler M, Abou Jamra R, Kamphausen SB, Bothe V, Potocki L, Olinger E, Sznajer Y, Wiame E, Thompson ML, Schroeder MC, Gooch C, Smith RA, Pandya A, Busch LM, Völker U, Hammer E, Wende K, Cogné B, Isidor B, Meiler J, Ripoll C, Bigou S, Laumonnier F, Hildebrand PW, Eichler EE, McWalter K, Krawitz PM, Roux-Dalvai F, Elgersma Y, Marcoux J, Bousquet MP, Droit A, Poschmann J, Grabrucker AM, Bolduc FV, Bézieau S, Ebstein F, Krüger E.

Nat Commun. 2025 Nov 26;16(1):10545. doi: 10.1038/s41467-025-65556-8. PMID: 41298377 Free PMC article.