The Jackson Laboratory

2025 Computational Sciences Publications

2025 Publications:

  1. Chari A, Hernan AE, Mahoney JM, Thornton R, Tahir MZ, Tisdall MM, Scott RC. Single unit-derived connectivity networks in tuberous sclerosis complex reveal propensity for network hypersynchrony driven by tuber-tuber interactions. Sci Rep. 2024;14(1):31654. PMID: 39738230; PMCID: PMC11686100.
    https://libkey.io/libraries/3075/39738230
  2. Saadaoui M, Djekidel MN, Murugesan S, Kumar M, Elhag D, Singh P, Kabeer BSA, Marr AK, Kino T, Brummaier T, McGready R, Nosten F, Chaussabel D, Terranegra A, Al Khodor S. Exploring the composition of placental microbiome and its potential origin in preterm birth. Front Cell Infect Microbiol. 2024;14:1486409. PMID: 39885963; PMCID: PMC11779731.
    https://libkey.io/libraries/3075/39885963
  3. Abraham DJ, Black CM, Denton CP, Distler JHW, Domsic R, Feghali-Bostwick C, Gourh P, Hinchcliff M, Kolling Ft, Kuwana M, Lafyatis R, Landegren U, Mahoney JM, Martin J, Matucci-Cerinic M, McMahan ZH, Mora AL, Mouthon L, Rabinovitch M, Rojas M, Rubin K, Trojanowska M, Varga J, Whitfield ML, Gabrielli A, Krieg T. An international perspective on the future of systemic sclerosis research. Nat Rev Rheumatol. 2025;21(3):174-87. PMID: 39953141. https://libkey.io/libraries/3075/39953141

  4. Adli M, Przybyla L, Burdett T, Burridge PW, Cacheiro P, Chang HY, Engreitz JM, Gilbert LA, Greenleaf WJ, Hsu L, Huangfu D, Hung LH, Kundaje A, Li S, Parkinson H, Qiu X, Robson P, Schürer SC, Shojaie A, Skarnes WC, Smedley D, Studer L, Sun W, Vidović D, Vierbuchen T, White BS, Yeung KY, Yue F, Zhou T, The MorPhiC Consortium. MorPhiC Consortium: towards functional characterization of all human genes. Nature. 2025;638(8050):351-9. PMID: 39939790. https://libkey.io/libraries/3075/39939790

  5. Delorme AE, Poirion OB, Lebreton L, le Gac PY, Kāne K, Royer SJ. A year-long field study of buried plastics reveals underestimation of plastic pollution on Hawaiian beaches. Mar Pollut Bull. 2025;214:117712. PMID: 40020394. https://libkey.io/libraries/3075/40020394

  6. Leclair NK, Brugiolo M, Park S, Devoucoux M, Urbanski L, Angarola BL, Yurieva M, Anczuków O. Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects. Nat Commun. 2025;16(1):1670. PMID: 39955311; PMCID: PMC11829967. https://libkey.io/libraries/3075/39955311

  7. Kabeer BAK, Subba B, Rinchai D, Toufiq M, Khan T, Yurieva M, Chaussabel D. From gene modules to gene markers: an integrated AI-human approach selects CD38 to represent plasma cell-associated transcriptional signatures. Front Med (Lausanne). 2025;12:1510431. PMID: 40144871; PMCID: PMC11936944. https://libkey.io/libraries/3075/40144871

  8. Khalife MR, Villarin C, Ruiz JM, McClelland SA, Rabbo KA, Mahoney JM, Scott RC, Hernan AE. Melanocortin 4 Receptor-Dependent Mechanism of ACTH in Preventing Anxiety-Like Behaviors and Normalizing Astrocyte Proteins after Early Life Seizures. eNeuro. 2025;12(3):ENEURO.0564-24.2025. PMID: 40015967; PMCID: PMC11897861. https://libkey.io/libraries/3075/40015967

  9. Alfaki M, Toufiq M, Kaavya S, Mathayan M, Palaniappan AN, Deenadayalan A, Bethunaickan R, Boughorbel S, Zerbib Y, Rinchai D, Garand M, Chaussabel D, Kabeer BSA. Deciphering the Role of Kruppel-like Factor 9 in Sepsis and Immunity: Perspectives from Joint Collective Omics Data and a Literature Review. Texila Int J Public Health. 2025;13(1). PMID: 10.21522/TIJPH.2013.13.01.Art092. https://libkey.io/libraries/3075/10.21522/TIJPH.2013.13.01.Art092

  10. Gunes I, Bernstein EJ, Cowper SE, Panse G, Pradhan N, Camacho LD, Page N, Bundschuh E, Williams A, Carns M, Aren K, Fantus S, Volkmann ER, Bukiri H, Correia C, Kolachalama VB, Wilson FP, Mawe S, Mahoney JM, Hinchcliff M. Neural network analysis as a novel skin outcome in a trial of belumosudil in patients with systemic sclerosis. Arthritis Res Ther. 2025;27(1):85. PMID: 40217251; PMCID: PMC11987334. https://libkey.io/libraries/3075/40217251

  11. Ahmad F, Uzair SA, Lakshmanan AP, Alabduljabbar S, Ahmed SH, Kabeer BSA, Marr AK, Kino T, Brummaier T, McGready R, Nosten F, Chaussabel D, Khodor SA, Terranegra A. Placental and Cord Blood DNA Methylation Changes Associated With Gestational Diabetes Mellitus in a Marginalized Population: The Untold Role of Saturated Fats. Mol Nutr Food Res. 2025;69(12):e70058. PMID: 40270325; PMCID: PMC12189174. https://libkey.io/libraries/3075/40270325

  12. Cabel CR, Guzman BA, Alizadeh E, Li S, Holberg C, Wichaidit C, Cusanovich DA, Paek AL, Thatcher GRJ, Van Doorslaer K, Nargi RS, Sutton RE, Suryadevara N, Crowe JE, Jr., Carnahan RH, Campos SK, Thorne CA. Cell-based high-content approach for SARS-CoV-2 neutralization identifies unique monoclonal antibodies and PI3K pathway inhibitors. Front Cell Dev Biol. 2025;13:1538934. PMID: 40486909; PMCID: PMC12142043. https://libkey.io/libraries/3075/40486909

  13. Ravera F, Dameri M, Lombardo I, Stabile M, Becherini P, Fallani N, Scarsi C, Cigolini B, Gentilcore G, Domnich A, Zullo L, Cella E, Francia G, Montanari E, Orsi A, Bellodi A, Ferrando F, Rinchai D, Ballerini F, Bruzzone B, Chaussabel D, Grivel JC, Genova C, Lemoli RM, Bedognetti D, Ballestrero A, Ferrando L, Zoppoli G. Biological modifications of the immune response to COVID-19 vaccine in patients treated with rituximab and immune checkpoint inhibitors. Cell Rep. 2025;44(7):115838. PMID: 40543041. https://libkey.io/libraries/3075/40543041

  14. Scott RC, Hsieh J, McTague A, Mahoney JM, Christian-Hinman CA. Merritt-Putnam Symposium | Developmental and Epileptic Encephalopathies-Current Concepts and Novel Approaches. Epilepsy Curr. 2025;25(3):229-35. PMID: 40161506; PMCID: PMC11948268. https://libkey.io/libraries/3075/40161506

  15. Aydin S, Skelly DA, Dewey HB, Mahoney JM, Choi T, Reinholdt LG, Baker CL, Munger SC. Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells. G3 (Bethesda). 2025;15(7). PMID: 40327589; PMCID: PMC12239603. https://libkey.io/libraries/3075/40327589

  16. Chew T, Pelaia TM, Phu AL, Teoh S, Wang Y, Deshpande N, Kim K, Herwanto V, Gunawan, Karvunidis T, Zerbib Y, Short KR, Macdonald S, Thevarajan I, Rinchai D, Kuan WS, Knippenberg B, Iredell J, Britton PN, Hutchings O, Britton WJ, Eden JS, Orde S, Tang B, McLean A, Chaussabel D, Schughart K, Shojaei M. Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset. Sci Data. 2025;12(1):1175. PMID: 40640204; PMCID: PMC12246199. https://libkey.io/libraries/3075/40640204

  17. Niyonkuru E, Caufield JH, Carmody LC, Gargano MA, Toro S, Whetzel PL, Blau H, Soto Gomez M, Casiraghi E, Chimirri L, Reese JT, Valentini G, Haendel MA, Mungall CJ, Robinson PN. Leveraging generative AI to assist biocuration of medical actions for rare disease. Bioinform Adv. 2025;5(1):vbaf141. PMID: 40621601; PMCID: PMC12228962. https://libkey.io/libraries/3075/40621601

  18. Tyler AL, Mahoney JM, Keller MP, Baker CN, Gaca M, Srivastava A, Gyuricza IG, Braun MJ, Rosenthal NA, Attie AD, Churchill GA, Carter GW. Transcripts with high distal heritability mediate genetic effects on complex metabolic traits. Nat Commun. 2025;16(1):5507. PMID: 40595617; PMCID: PMC12216720. https://libkey.io/libraries/3075/40595617

  19. Han C, Zhang Z, Crosse EI, Sajedi S, Lu B, Wang X, Karma S, Kostich M, Rajendran SH, Udy DB, Chen S, Arnuk A, Lawal AE, Koenig KR, McKenna M, Reville PK, Abbas HA, Abdel-Wahab O, Miura P, Bradley RK, Wang E. An Isoform-Specific RUNX1C-BTG2 Axis Governs AML Quiescence and Chemoresistance. Blood Cancer Discov. 2025;6(5):464-83. PMID: 40632085. https://libkey.io/libraries/3075/40632085

  20. Hoyt LR, Liu E, Olson EC, Jacobsen DR, Siniscalco ER, Krier-Burris RA, Greenfield KG, McBride CD, Alfajaro MM, Amat JAR, Zhao Z, Xu L, Philip V, Verma A, Fourati S, Senger DL, Zhang L, Bunyavanich S, Glass SE, Coffey RJ, Wilen CB, Williams A, Eisenbarth SC. Cysteinyl leukotrienes stimulate gut absorption of food allergens to promote anaphylaxis in mice. Science. 2025;389(6760):eadp0240. PMID: 40773557; PMCID: PMC12333546. https://libkey.io/libraries/3075/40773557

  21. Li J, Deng Y, Gasser M, Zhu J, Walker EM, Sidarala V, Reck EC, Hubers DL, Pasmooij MB, Shin CS, Bandesh K, Motakis E, Nargund S, Kursawe R, Basrur V, Nesvizhskii AI, Stitzel ML, Chan DC, Rutter GA, Soleimanpour SA. LONP1 regulation of mitochondrial protein folding provides insight into beta cell failure in type 2 diabetes. Nat Metab. 2025;7(8):1570-92. PMID: 40691304; PMCID: PMC12373512 and is a consultant for Novo Nordisk. G.A.R. has received grant funding from Sun Pharmaceuticals and Les Laboratoires Servier and is a consultant for Sun Pharmaceuticals. A.I.N. receives royalties from the University of Michigan for the sale of MSFragger and IonQuant software licences to commercial entities. All licence transactions are managed by the University of Michigan Innovation Partnerships office; all proceeds are subject to university technology transfer policy. The other authors declare no competing interests. https://libkey.io/libraries/3075/40691304

  22. Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Scholz S, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Song Y, Soylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. Complex genetic variation in nearly complete human genomes. Nature. 2025;644(8076):430-41. PMID: 40702183; PMCID: PMC12350169 C. Lee is a scientific advisory board member of Nabsys. S.K. has received travel funds to speak at events hosted by ONT. J.O.K., T.M. and D.P. have previously disclosed a patent application (no. EP19169090) relevant to Strand-seq. The other authors declare no competing interests. https://libkey.io/libraries/3075/40702183

  23. Mullis MN, Wright KM, Raj A, Gatti DM, Reifsnyder PC, Flurkey K, Archer JR, Robinson L, Di Francesco A, Svenson KL, Korstanje R, Harrison DE, Ruby JG, Churchill GA. Analysis of lifespan across diversity outbred mouse studies identifies multiple longevity-associated loci. Genetics. 2025;230(4):iyaf081. PMID: 40326784; PMCID: PMC12342377. https://libkey.io/libraries/3075/40326784

  24. Yu M, Philip V. mzrtsim: Raw Data Simulation for Reproducible Gas/Liquid Chromatography-Mass Spectrometry-Based Nontargeted Metabolomics Data Analysis. Anal Chem. 2025;97(32):17309-14. PMID: 40762567. https://libkey.io/libraries/3075/40762567

  25. Chimirri L, Caufield JH, Bridges Y, Matentzoglu N, Gargano M, Cazalla M, Chen S, Danis D, Dingemans AJM, Gehle K, Gehle P, Graefe ASL, Gu W, Ladewig MS, Lapunzina P, Nevado J, Niyonkuru E, Ogishima S, Seelow D, Tenorio Castaño JA, Turnovec M, de Vries BBA, Wang K, Wissink K, Yüksel Z, Zucca G, Haendel MA, Mungall CJ, Reese J, Robinson PN. Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases. EBioMedicine. 2025;121:105957. PMID: 41092581; PMCID: PMC12552141. https://libkey.io/libraries/3075/41092581

  26. Ho CH, Dippel MA, McQuade MS, Nguyen LP, Mishra A, Pribitzer S, Hardy S, Chandok H, Chardon FM, McDiarmid TA, DeBerg HA, Buckner JH, Shendure J, de Boer CG, Guo MH, Tewhey R, Ray JP. Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks. Nat Genet. 2025;57(10):2536-45. PMID: 40968290; PMCID: PMC12513834. https://libkey.io/libraries/3075/40968290

  27. Khan T, Toufiq M, Yurieva M, Indrawattana N, Jittmittraphap A, Kosoltanapiwat N, Pumirat P, Sukphopetch P, Vanaporn M, Palucka K, Syed Ahamed Kabeer B, Rinchai D, Chaussabel D. Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation. Bioinformatics. 2025;41(10). PMID: 41071041; PMCID: PMC12548045. https://libkey.io/libraries/3075/41071041

  28. Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, Elisseeff J, Farzad N, Fertig EJ, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur NK, Li D, Ma A, Ma Q, Menon V, Mitchell JT, Mora AL, Nagaraj S, Nelson AC, Niedernhofer LJ, Rojas M, Taha HB, Wang J, Wang S, Wu PH, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams PD, Aguayo-Mazzucato C, Baker DJ, Benz C, Bernlohr DA, Bueno M, Chen J, Childs BG, Chuang JH, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn WF, Franco AC, Furman D, Garovic V, Halene S, Herman AB, Hertzel AV, Iwasaki K, Jeon H, Kang JW, Karmakar S, Kirkland JL, Korstanje R, Kummerfeld E, Lee JH, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos JF, Peters ST, Rahman I, Ramasamy R, Rindone AN, Robbins PD, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer MJ, Schilling B, Schmidt EL, Schneider K, Sengupta K, Shu J, So PTC, Sun L, Tchkonia T, Teneche MG, Vanegas N, Wang J, Xie J, Yin S, Zhang K, Zhu Q, Fan R, SenNet Consortium. Advancing biological understanding of cellular senescence with computational multiomics. Nat Genet. 2025;57(10):2381-94. PMID: 40954249. https://libkey.io/libraries/3075/40954249

  29. Widmayer SJ, Wooldridge LK, Swanzey E, Barter M, Snow C, Saul M, Meng Q, Dumont B, Reinholdt L, Gatti DM. Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses. Mamm Genome. 2025;36(4):1063-80. PMID: 40593333; PMCID: PMC12365916. https://libkey.io/libraries/3075/40593333

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