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    2025

  1. A comprehensive benchmark of single-cell Hi-C embedding tools

    Plummer, D; Lang, X; Zhang, S; Li, Y; Li, J; Jin, F;
    2025;  
    Nature Communications;  
    Volume: 16;  
    Issue: 1;  
  2. 2025;  
    Scientific Reports;  
    Volume: 15;  
    Issue: 1;  
  3. Sleep, pericyte subtypes and cognitive decline in adults with and without Alzheimer's disease

    Hamid, M; Saha Detroja, T; Tripathy, SJ; Menon, V; Xu, J; Yu, L; Wang, Y; Buchman, AS; Bennett, DA; De Jager, PL; Lim, ASP;
    2025;  
    Brain: A Journal of Neurology;  
    Volume: 148;  
    Issue: 9;  
  4. Alzheimer's disease transcriptional landscape in ex vivo human microglia

    Kosoy, R; Fullard, JF; Bendl, J; Kleopoulos, SP; Shao, Z; Argyriou, S; Mathur, D; Psychogyiou, K; Malakates, P; Vicari, J; Ma, Y; Humphrey, J; Brophy, E; Raj, T; Katsel, P; Voloudakis, G; Lee, D; Bennett, DA; Haroutunian, V; Hoffman, GE; Roussos, P;
    2025;  
    Nature Neuroscience;  
    Volume: 28;  
    Issue: 9;  
  5. Ms4a4a deficiency ameliorates plaque pathology in a mouse model of amyloid accumulation

    Danhash, EP; Verbeck, AC; Western, D; Díaz-Pacheco, AS; Galasso, G; You, S; Huang, G; Starr, E; Miller, N; Nadarajah, CJ; Tiemann Powles, S; Musiek, ES; Herz, J; Iyer, AK; Cirrito, J; Cruchaga, C; Karch, CM;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 8;  
  6. Uncovering Ethnicity-Specific Recessive Loci for Alzheimer's Disease in 89 Dominican Families Using Family-Based WGS Analysis

    Lee, S; Hecker, J; Vardarajan, BN; Kelly, RS; Prince, N; Mullin, K; Lutz, SM; Hahn, G; Lasky-Su, J; Mayeux, RP; Tanzi, RE; Lange, C; Prokopenko, D;
    2025;  
    Genetic Epidemiology;  
    Volume: 49;  
    Issue: 5;  
  7. Exploring potential mechanisms of an African protective locus for Alzheimer's disease in APOEε4 carriers

    Bertholim-Nasciben, L; Nuytemans, K; Van Booven, D; Rajabli, F; Moura, S; Ramirez, AM; Parker, GS; Dykxhoorn, DM; Wang, L; Scott, WK; Davis, DA; Vontell, RT; McInerney, KF; Cuccaro, ML; Byrd, GS; Haines, JL; Gearing, M; Adams, LD; Pericak-Vance, MA; Young, JI; Griswold, AJ; Vance, JM;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 7;  
  8. CLU alleviates Alzheimer's disease-relevant processes by modulating astrocyte reactivity and microglia-dependent synaptic density

    Lish, AM; Grogan, EFL; Benoit, CR; Pearse, RV; Heuer, SE; Luquez, T; Orme, GA; Galle, PC; Milinkeviciute, G; Green, KN; Alexander, KD; Fancher, SB; Stern, AM; Fujita, M; Bennett, DA; Seyfried, NT; De Jager, PL; Menon, V; Young-Pearse, TL;
    2025;  
    Neuron;  
    Volume: 113;  
    Issue: 12;  
  9. Large-scale plasma proteomic profiling unveils diagnostic biomarkers and pathways for Alzheimer's disease

    Heo, G; Xu, Y; Wang, E; Ali, M; Oh, HS; Moran-Losada, P; Anastasi, F; González Escalante, A; Puerta, R; Song, S; Timsina, J; Liu, M; Western, D; Gong, K; Chen, Y; Kohlfeld, P; Flynn, A; Thomas, AG; Lowery, J; Morris, JC; Holtzman, DM; Perlmutter, JS; Schindler, SE; Vilor-Tejedor, N; Suárez-Calvet, M; García-González, P; Marquié, M; Fernández, MV; Boada, M; Cano, A; Ruiz, A; Zhang, B; Bennett, DA; Benzinger, T; Wyss-Coray, T; Ibanez, L; Sung, YJ; Cruchaga, C;
    2025;  
    Nature Aging;  
    Volume: 5;  
    Issue: 6;  
  10. Distinct systemic impacts of Aβ42 and Tau revealed by whole-organism snRNA-seq

    Park, Y; Lu, T; Jackson, T; Goodman, LD; Ran, L; Chen, J; Liang, C; Harrison, E; Ko, C; Chen, X; Wang, B; Hsu, A; Ochoa, E; Bieniek, KF; Yamamoto, S; Zhu, Y; Zheng, H; Qi, Y; Bellen, HJ; Li, H;
    2025;  
    Neuron;  
  11. Multi-cohort cerebrospinal fluid proteomics identifies robust molecular signatures across the Alzheimer disease continuum

    Ali, M; Timsina, J; Western, D; Liu, M; Beric, A; Budde, J; Do, A; Heo, G; Wang, L; Gentsch, J; Schindler, SE; Morris, JC; Holtzman, DM; Ruiz, A; Alvarez, I; Aguilar, M; Pastor, P; Rutledge, J; Oh, H; Wilson, EN; Guen, YL; Khalid, RR; Knight Alzheimer Disease Research Center (Knight ADRC); Alzheimer Disease Neuroimaging Initiative (ADNI); Fundació ACE Alzheimer Center Barcelona (FACE); Barcelona-1; Stanford Alzheimer Disease Research Center (Stanford ADRC); Robins, C; Pulford, DJ; Tarawneh, R; Ibanez, L; Wyss-Coray, T; Sung, YJ; Cruchaga, C;
    2025;  
    Neuron;  
    Volume: 113;  
    Issue: 9;  
  12. Alzheimer's disease protective allele of Clusterin modulates neuronal excitability through lipid-droplet-mediated neuron-glia communication

    Zhao, X; Li, Y; Zhang, S; Sudwarts, A; Zhang, H; Kozlova, A; Moulton, MJ; Goodman, LD; Pang, ZP; Sanders, AR; Bellen, HJ; Thinakaran, G; Duan, J;
    2025;  
    Molecular Neurodegeneration;  
    Volume: 20;  
    Issue: 1;  
  13. Ubiquitin-proteasome system in the different stages of dominantly inherited Alzheimer's disease

    Liu, H; Bui, Q; Hassenstab, J; Gordon, BA; Benzinger, TLS; Timsina, J; Sung, YJ; Karch, C; Renton, AE; Daniels, A; Morris, JC; Xiong, C; Ibanez, L; Perrin, RJ; Llibre-Guerra, JJ; Day, GS; Supnet-Bell, C; Xu, X; Berman, SB; Chhatwal, JP; Ikeuchi, T; Kasuga, K; Niimi, Y; Huey, ED; Schofield, PR; Brooks, WS; Ryan, NS; Jucker, M; Laske, C; Levin, J; Vöglein, J; Roh, JH; Lopera, F; Bateman, RJ; Cruchaga, C; McDade, EM; For DIAN study team;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 5;  
  14. Association of dietary fatty acids with longitudinal change in plasma-based biomarkers of Alzheimer's disease

    Hoost, SS; Honig, LS; Kang, MS; Bahl, A; Lee, AJ; Sanchez, D; Reyes-Dumeyer, D; Lantigua, RA; Dage, JL; Brickman, AM; Manly, JJ; Mayeux, R; Gu, Y;
    2025;  
    The Journal of Prevention of Alzheimer's Disease..;  
    Volume: 12;  
    Issue: 5;  
  15. Ubiquitin-proteasome system in the different stages of dominantly inherited Alzheimer's disease

    Liu, H; Bui, Q; Hassenstab, J; Gordon, BA; Benzinger, TLS; Timsina, J; Sung, YJ; Karch, C; Renton, AE; Daniels, A; Morris, JC; Xiong, C; Ibanez, L; Perrin, RJ; Llibre-Guerra, JJ; Day, GS; Supnet-Bell, C; Xu, X; Berman, SB; Chhatwal, JP; Ikeuchi, T; Kasuga, K; Niimi, Y; Huey, ED; Schofield, PR; Brooks, WS; Ryan, NS; Jucker, M; Laske, C; Levin, J; Vöglein, J; Roh, JH; Lopera, F; Bateman, RJ; Cruchaga, C; McDade, EM; For DIAN study team;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 5;  
  16. Computational and functional prioritization identifies genes that rescue behavior and reduce tau protein in fly and human cell models of Alzheimer disease

    Stephens, MC; Li, J; Mair, M; Moore, J; Zhu, K; Tarkunde, A; Amoh, B; Perez, AM; Bhakare, A; Guo, F; Shulman, JM; Al-Ramahi, I; Botas, J;
    2025;  
    American Journal of Human Genetics;  
    Volume: 112;  
    Issue: 5;  
  17. A cerebrospinal fluid synaptic protein biomarker for prediction of cognitive resilience versus decline in Alzheimer's disease

    Oh, HS; Urey, DY; Karlsson, L; Zhu, Z; Shen, Y; Farinas, A; Timsina, J; Duggan, MR; Chen, J; Guldner, IH; Morshed, N; Yang, C; Western, D; Ali, M; Le Guen, Y; Trelle, A; Herukka, S; Rauramaa, T; Hiltunen, M; Lipponen, A; Luikku, AJ; Poston, KL; Mormino, E; Wagner, AD; Wilson, EN; Channappa, D; Leinonen, V; Stevens, B; Ehrenberg, AJ; Gottesman, RF; Coresh, J; Walker, KA; Zetterberg, H; Bennett, DA; Franzmeier, N; Hansson, O; Cruchaga, C; Wyss-Coray, T;
    2025;  
    Nature Medicine;  
    Volume: 31;  
    Issue: 5;  
  18. 2025;  
    Nature Genetics;  
    Volume: 57;  
    Issue: 5;  
  19. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

    Jensen, TD; Ni, B; Reuter, CM; Gorzynski, JE; Fazal, S; Bonner, D; Ungar, RA; Goddard, PC; Raja, A; Ashley, EA; Bernstein, JA; Zuchner, S; Undiagnosed Diseases Network; Greicius, MD; Montgomery, SB; Schatz, MC; Wheeler, MT; Battle, A;
    2025;  
    Genome Research;  
    Volume: 35;  
    Issue: 4;  
  20. Integrative network analysis reveals novel moderators of Aβ-Tau interaction in Alzheimer's disease

    Kitani, A; Matsui, Y; Alzheimer’s Disease Neuroimaging Initiative;
    2025;  
    Alzheimer's Research & Therapy;  
    Volume: 17;  
    Issue: 1;  
  21. APOE and Alzheimer's disease and related dementias risk among 12,221 Hispanics/Latinos

    Barral, S; Yang, Z; Phillips, N; Barber, RC; Brickman, AM; Honig, LS; Cieza, B; Reyes-Dumeyer, D; Mayeux, R; Rajabli, F; Cuccaro, ML; Vance, JM; Arango, SM; Samper-Ternent, R; Obregon, AM; Montesinos, R; Soto-Añari, M; Duran, JC; Cusicanqui, M; Velazquez, IZJ; Marca, V; Illanes-Manrique, M; Cornejo-Olivas, M; Pericak-Vance, M; Wong, R; O'Bryant, S; Custodio, N; Tosto, G;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 4;  
  22. Interactions between menopause and high-fat diet on cognition and pathology in a mouse model of Alzheimer's disease

    Abi-Ghanem, C; Kelly, RD; Groom, EA; Valerian, CG; Paul, AS; Thrasher, CA; Salinero, AE; Batchelder, MR; Lafrican, JJ; Wang, M; Smith, RM; Temple, S; Zuloaga, DG; Zuloaga, KL;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 3;  
  23. Plasma protein risk scores for mild cognitive impairment and Alzheimer's disease in the Framingham heart study

    Rehman, H; Ang, TFA; Tao, Q; Au, R; Farrer, LA; Qiu, WQ; Zhang, X; Alzheimer's Disease Neuroimaging Initiative;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 3;  
  24. Contributions of Genetic Variation in Astrocytes to Cell and Molecular Mechanisms of Risk and Resilience to Late-Onset Alzheimer's Disease

    Lee, H; Pearse, RV; Lish, AM; Pan, C; Augur, ZM; Terzioglu, G; Gaur, P; Liao, M; Fujita, M; Tio, ES; Duong, DM; Felsky, D; Seyfried, NT; Menon, V; Bennett, DA; De Jager, PL; Young-Pearse, TL;
    2025;  
    Glia;  
  25. Comparing Alzheimer's genes in African, European, and Amerindian induced pluripotent stem cell-derived microglia

    Moura, S; Nasciben, LB; Ramirez, AM; Coombs, L; Rivero, J; Van Booven, DJ; DeRosa, BA; Hamilton-Nelson, KL; Whitehead, PL; Adams, LD; Starks, TD; Mena, PR; Illanes-Manrique, M; Tejada, S; Byrd, GS; Cornejo-Olivas, MR; Feliciano-Astacio, BE; Nuytemans, K; Wang, L; Pericak-Vance, MA; Dykxhoorn, DM; Rajabli, F; Griswold, AJ; Young, JI; Vance, JM;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 2;  
  26. Benchmarking of a multi-biomarker low-volume panel for Alzheimer's disease and related dementia research

    Ibanez, L; Liu, M; Beric, A; Timsina, J; Kohlfeld, P; Bergmann, K; Lowery, J; Sykora, N; Sanchez-Montejo, B; Brock, W; Budde, JP; Bateman, RJ; Barthelemy, N; Schindler, SE; Holtzman, DM; Benzinger, TLS; Xiong, C; Tarawneh, R; Moulder, K; Morris, JC; Sung, YJ; Cruchaga, C;
    2025;  
    Alzheimer's & Dementia: The Journal of the Alzheimer's Association;  
    Volume: 21;  
    Issue: 2;  
  27. Microglial lipid phosphatase SHIP1 limits complement-mediated synaptic pruning in the healthy developing hippocampus

    Matera, A; Compagnion, A; Pedicone, C; Kotah, JM; Ivanov, A; Monsorno, K; Labouèbe, G; Leggio, L; Pereira-Iglesias, M; Beule, D; Mansuy-Aubert, V; Williams, TL; Iraci, N; Sierra, A; Marro, SG; Goate, AM; Eggen, BJL; Kerr, WG; Paolicelli, RC;
    2025;  
    Immunity;  
    Volume: 58;  
    Issue: 1;  
  28. CRISPRi-based screens in iAssembloids to elucidate neuron-glia interactions

    Li, E; Benitez, C; Boggess, SC; Koontz, M; Rose, IVL; Martinez, D; Dräger, N; Teter, OM; Samelson, AJ; Pierce, N; Ullian, EM; Kampmann, M;
    2025;  
    Neuron;  
  29. The Dynamics of Cognitive Decline towards Alzheimer's Disease Progression: Results from ADSP-PHC's Harmonized Cognitive Composites

    Kang, K; Zhang, P; Dumitrescu, L; Mukherjee, S; Lee, ML; Choi, S; Trittschuh, EH; Mez, J; Saykin, AJ; Gifford, KA; Buckley, RF; Gao, X; Di, J; Crane, PK; Hohman, TJ; Liu, D;
    2025;  
    medRxiv: The Preprint Server for Health Sciences;  
  30. regionalpcs improve discovery of DNA methylation associations with complex traits

    Eulalio, T; Sun, MW; Gevaert, O; Greicius, MD; Montine, TJ; Nachun, D; Montgomery, SB;
    2025;  
    Nature Communications;  
    Volume: 16;  
    Issue: 1;  
  31. Patient stratification by genetic risk in Alzheimer's disease is only effective in the presence of phenotypic heterogeneity

    Euesden, J; Ali, M; Robins, C; Surendran, P; Gormley, P; Alzheimer’s Disease Neuroimaging Initiative (ADNI); Pulford, D; Cruchaga, C;
    2025;  
    PloS One;  
    Volume: 20;  
    Issue: 1;  
  32. LD-informed deep learning for Alzheimer's gene loci detection using WGS data

    Jo, T; Bice, P; Nho, K; Saykin, AJ; Alzheimer's Disease Sequencing Project;
    2025;  
    Alzheimer's & Dementia (New York, N. Y.);  
    Volume: 11;  
    Issue: 1;