2025 Computational Sciences Publications

2025 Publications:

1. Andrews JM, Lloyd MW, Neuhauser SB, Bundy M, Jocoy EL, Airhart SD, Bult CJ, Evrard YA, Chuang JH, Baker S. STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication. Bioinformatics. 2024;40(12). PMID: 39589865; PMCID: PMC11634538.
   https://libkey.io/libraries/3075/39589865
2. Zhao Y, Agyemang D, Liu Y, Mahoney M, Li S. Quantifying interpretation reproducibility in Vision Transformer models with TAVAC. Sci Adv. 2024;10(51):eabg0264. PMID: 39705362; PMCID: PMC11661421.
   https://libkey.io/libraries/3075/39705362
3. 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
4. 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
5. 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

6. 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

7. 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

8. 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

9. 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

10. 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